(partial answer)
Simplification
Let's start with an intuitive simplification. The cubes must be stacked in independent "layers", where each layer "sits" on $y=k$ for some integer $k$.
Now, given a sphere with a certain radius and offset, notice that the cubes in each layer must fit inside a cylinder.
Example
There are 3 cylinder-shaped layers here: red, yellow, and blue. The y-axis passes through the center of each cylinder.
In this example, the layers have radii $1.118$, $1.688$, and $0.80564$. According to this page, these layers can contain $2$, $6$, and $1$ cubes respectively. So, this sphere contains $9$ cubes in total. This happens to be optimal given the "layers" constraint. (It might be possible to show that no axis-aligned cube configuration can fit $9$ cubes in a sphere of radius $1.7915$). Note that the middle layer in this example contains a non-axis-aligned cube.
Per-layer view
For convenience, here's what each layer looks like (not to scale):
Optimal radii (under "layers" constraint)
Here's a table of optimal radii for packing cubes in a sphere, with the "layers" constraint. The numbers in curly braces indicate the per-layer cube count. Note that the radius/y-offset values are only accurate to about 3 or 4 digits, since the reference page provides similarly low-precision values.
1: {1} r = 0.865938 y-offset = 0.5
2: {1,1} r = 1.22468 y-offset = 0
3: {3} r = 1.38165 y-offset = 0.5
4: {1,3} r = 1.47084 y-offset = 0.289774
5: {1,4} r = 1.54602 y-offset = 0.374887
6: {3,3} r = 1.63063 y-offset = 0
7: {1,5,1} r = 1.65827 y-offset = 0.5
8: {4,4} r = 1.73188 y-offset = 0
9: {1,6,2} r = 1.79151 y-offset = 0.600145
10: {1,6,3} r = 1.83486 y-offset = 0.693183
11: {2,7,2} r = 1.87081 y-offset = 0.5
12: {2,7,3} r = 1.9259 y-offset = 0.56817
13: {2,7,4} r = 1.97237 y-offset = 0.624912
14: {1,7,6} r = 2.01939 y-offset = 0.891583
15: {4,8,3} r = 2.04565 y-offset = 0.478272
16: {4,8,4} r = 2.06141 y-offset = 0.5
17: {4,8,5} r = 2.12283 y-offset = 0.583361
18: {5,9,4} r = 2.14767 y-offset = 0.453592
19: {6,9,4} r = 2.17157 y-offset = 0.366146
20: {5,10,5} r = 2.17935 y-offset = 0.5
21: {5,10,6} r = 2.21988 y-offset = 0.558297
22: {6,10,6} r = 2.25817 y-offset = 0.5
23: {6,11,6} r = 2.26976 y-offset = 0.5
24: {6,12,6} r = 2.29122 y-offset = 0.5
25: {7,12,6} r = 2.30552 y-offset = 0.438123
26: {7,12,7} r = 2.34461 y-offset = 0.5
27: {2,10,11,4} r = 2.38964 y-offset = 0.100789
28: {2,10,12,4} r = 2.40112 y-offset = 0.124962
29: {3,10,12,4} r = 2.4268 y-offset = 0.056792
30: {3,11,12,4} r = 2.43954 y-offset = 0.024475
31: {4,12,11,4} r = 2.44941 y-offset = 0.99995
32: {4,12,12,4} r = 2.44943 y-offset = 1
33: {4,12,12,5} r = 2.50068 y-offset = 0.0625206
34: {3,12,13,6} r = 2.51134 y-offset = 0.143302
35: {4,12,13,6} r = 2.53686 y-offset = 0.106243
36: {5,13,13,5} r = 2.56377 y-offset = 1
37: {5,13,13,6} r = 2.58387 y-offset = 0.0437229
38: {6,13,13,6} r = 2.61713 y-offset = 1
39: {4,12,15,8} r = 2.64823 y-offset = 0.239136
40: {4,13,15,8} r = 2.65881 y-offset = 0.223263
41: {2,12,16,10,1} r = 2.68245 y-offset = 0.438368
42: {1,12,16,12,1} r = 2.69253 y-offset = 0.5
43: {2,12,16,12,1} r = 2.71008 y-offset = 0.468722
44: {7,15,15,7} r = 2.72325 y-offset = 0
45: {2,12,17,12,2} r = 2.7386 y-offset = 0.5
46: {1,12,17,13,3} r = 2.74689 y-offset = 0.595535
47: {4,13,17,12,1} r = 2.76409 y-offset = 0.375037
48: {3,13,18,12,2} r = 2.7907 y-offset = 0.47569
49: {3,13,18,13,2} r = 2.80273 y-offset = 0.489245
50: {3,13,18,13,3} r = 2.81228 y-offset = 0.5
51: {1,12,17,15,6} r = 2.83083 y-offset = 0.736065
52: {6,15,18,12,1} r = 2.83545 y-offset = 0.274248
53: {1,12,18,15,7} r = 2.86339 y-offset = 0.774735
54: {5,15,19,13,2} r = 2.87775 y-offset = 0.36579
55: {2,13,19,15,6} r = 2.88566 y-offset = 0.659555
56: {4,13,19,15,5} r = 2.91763 y-offset = 0.552087
57: {2,13,19,16,7} r = 2.9258 y-offset = 0.703776
58: {5,15,20,14,4} r = 2.93966 y-offset = 0.478315
59: {5,15,20,15,4} r = 2.94915 y-offset = 0.489566
60: {4,15,21,15,5} r = 2.95764 y-offset = 0.500389
61: {5,15,21,15,5} r = 2.95797 y-offset = 0.5
62: {7,16,21,14,4} r = 2.98152 y-offset = 0.37535
63: {7,16,21,15,4} r = 2.99809 y-offset = 0.396111
64: {4,15,21,17,7} r = 3.00946 y-offset = 0.62504
65: {6,16,21,16,6} r = 3.02161 y-offset = 0.5
66: {8,18,21,15,4} r = 3.04339 y-offset = 0.312951
67: {7,17,21,16,6} r = 3.04957 y-offset = 0.460214
68: {6,17,21,17,7} r = 3.07356 y-offset = 0.510109
69: {7,17,22,17,6} r = 3.07771 y-offset = 0.495015
70: {7,17,22,17,7} r = 3.08175 y-offset = 0.5
71: {7,17,22,18,7} r = 3.10877 y-offset = 0.533235
72: {7,18,23,17,7} r = 3.11626 y-offset = 0.482562
73: {7,18,23,18,7} r = 3.12459 y-offset = 0.5
74: {9,19,23,17,6} r = 3.14122 y-offset = 0.35655
75: {8,19,23,18,7} r = 3.15434 y-offset = 0.438972
76: {8,19,24,18,7} r = 3.15857 y-offset = 0.448213
77: {5,16,23,21,12} r = 3.17209 y-offset = 0.750014
78: {10,19,24,18,7} r = 3.18557 y-offset = 0.376805
79: {11,21,24,17,6} r = 3.18931 y-offset = 0.294015
80: {6,17,24,21,12} r = 3.19699 y-offset = 0.715035
81: {7,18,24,21,11} r = 3.21743 y-offset = 0.665459
82: {7,18,24,21,12} r = 3.22555 y-offset = 0.675249
83: {12,21,25,18,7} r = 3.24149 y-offset = 0.346821
84: {10,21,26,19,8} r = 3.25008 y-offset = 0.437294
85: {12,21,26,19,7} r = 3.26155 y-offset = 0.374451
86: {9,20,26,21,10} r = 3.26861 y-offset = 0.521296
87: {10,21,26,21,9} r = 3.27838 y-offset = 0.499823
88: {10,21,26,21,10} r = 3.27851 y-offset = 0.5
89: {10,21,27,21,10} r = 3.29911 y-offset = 0.5
90: {12,21,27,21,9} r = 3.30889 y-offset = 0.439071
91: {10,21,27,21,12} r = 3.31688 y-offset = 0.550105
92: {4,17,25,25,17,4} r = 3.34161 y-offset = 0
93: {4,17,25,26,17,4} r = 3.34961 y-offset = 0.0133453
94: {4,17,26,26,17,4} r = 3.35357 y-offset = 0
95: {5,17,26,26,17,4} r = 3.36314 y-offset = 0.968355
96: {4,17,26,26,18,5} r = 3.36773 y-offset = 0.043344
97: {6,18,26,26,17,4} r = 3.38293 y-offset = 0.931698
98: {4,17,26,27,18,6} r = 3.38884 y-offset = 0.0779653
99: {4,17,26,27,19,6} r = 3.39633 y-offset = 0.0879853
100: {7,19,27,26,17,4} r = 3.41088 y-offset = 0.896016
101: {5,18,27,27,18,6} r = 3.41887 y-offset = 0.0269029
102: {6,19,27,27,18,5} r = 3.42474 y-offset = 0.962031
103: {6,19,27,27,18,6} r = 3.44489 y-offset = 0.99701
104: {6,19,27,27,19,6} r = 3.44663 y-offset = 0
105: {4,17,27,28,21,8} r = 3.46141 y-offset = 0.159424
106: {8,21,28,27,18,4} r = 3.47742 y-offset = 0.86006
107: {7,20,28,27,19,6} r = 3.48771 y-offset = 0.947989
108: {7,21,28,27,19,6} r = 3.4989 y-offset = 0.935212
109: {6,19,28,28,21,7} r = 3.50764 y-offset = 0.0490244
110: {7,20,28,28,20,7} r = 3.51702 y-offset = 0
111: {3,17,27,29,23,12} r = 3.52237 y-offset = 0.278439
112: {7,21,28,28,21,7} r = 3.53514 y-offset = 0
113: {12,23,29,27,18,4} r = 3.54536 y-offset = 0.751339
114: {7,21,29,29,21,7} r = 3.55552 y-offset = 0
115: {4,18,27,30,24,12} r = 3.561 y-offset = 0.268229
116: {12,24,30,28,18,4} r = 3.57109 y-offset = 0.755163
117: {12,23,30,28,19,5} r = 3.57674 y-offset = 0.791655
118: {12,24,30,28,19,5} r = 3.58473 y-offset = 0.782746
119: {7,21,29,30,22,10} r = 3.59734 y-offset = 0.108
120: {7,21,29,30,23,10} r = 3.60337 y-offset = 0.118263
121: {12,24,30,29,20,6} r = 3.61222 y-offset = 0.836975
122: {12,24,30,29,21,6} r = 3.62226 y-offset = 0.849753
123: {12,24,30,29,21,7} r = 3.62557 y-offset = 0.853959
124: {12,24,31,29,21,7} r = 3.63433 y-offset = 0.843872
This table was computed by forcing the sphere to pass through $(x_0,y_0)$ and $(x_1,y_1)$ for $x_0$ and $x_1$ being members of the set of radii from the reference page, and $y_0 = 0$ and integer $y_1$.