Specifically Expected Answer:
The clue ---- |||| refers to a 4x4 grid where there are 4 words (4 letters each) horizontally, and the same grid gives the same words vertically.
This restriction fixes the possible values for each of the clues, which may have many matches in isolation.
1st word, Protons may be considered "indivisible, but not really" because they are made of quarks, but we can not split the Proton into 3 quarks. ATOM by Definition or Etymology, mean Indivisible, but we have been able to split that into Electrons, Protons and Neutrons.
2nd word, there may have been a wide variety of cloaks worn in Rome, but TOGA starts with T (2nd letter of ATOM)
3rd word, there may be many Different Possibilities, but not many start with O (3rd letter of ATOM). Anyway let us skip it for now.
4th word, 20 quires make a ream, but that will not start with M (last letter of ATOM). So the clue says "in reverse" so make that MAER, which starts with M.
Now it is a simple matter to fill in OGRE.
I seem to have initiated a MEME with this simple puzzle : "rand al'thor" was inspired to make a 5-word variant, then "Engineer Toast" made variants for sizes 6 & 7 & 8 , finally "Avon" made 6-word variants twice.