Header can win. Here is the quick answer with the more elaborate logic showing how I arrived at it after.
Quick answer
The setup is initially $HTHTH$. On his first turn, Header will add T on the end, making $HTHTHT$. Then he will flip the first $T$ to make $HHHTHT$.
On Tailer's turn, he can add either $T$ or $H$ at the front.
Lets try $T$ first. So, he will make $THHHTHT$. Now he must flip a section.
- If he flips the $HHH$ section, it now becomes $TTTTTHT$. If header plays $H$ and flips the first $H$, Tailer will be left with $TTTTTTTH$. No matter what letter is added, the section of $T$s is the only section that can be flipped, which leaves only $H$s, so Header will win.
- If he flips the middle $T$, then it now becomms $THHHHHT$. Header can play $H$ and flip all the interior $H$s to make $TTTTTTTH$, which is the same as the previous scenario.
- If he flips the last $H$, it becomes $THHHTTT$. Again, Header can add $H$ and flip the section of $H$s to make $TTTTTTTH$ - a guaranteed win for Header.
So now lets try adding $H$ instead. This makes $HHHHTHT$.
- If he flips first section of 4 $H$s, it becomes $TTTTTHT$. Header can again add an $H$ and flip the interior $H$ to get a winning position.
- If he flips the first $T$, then he leave $HHHHHHT$. Header wins easily by adding $H$ and flipping the $T$ to leave all $H$s.
- If he flips the last $H$, it becomes $HHHHTTT$. Again, Header wins easily by adding $H$ and flipping the section of $T$s.
Long Answer
For notation, we will use a version of regex symbols. $^*$ means the previous coin is repeated 0 or more times (i.e. appears at least once).
For example, $HT^*H^*$ can be used to represent $HTH$ or $HHHTTTH$ or $HHTTHH$.
For the following scenarios, Header plays on the end of the string of coins, and Tailer plays at the front.
We will break the solution down to the component parts.
Single section of coins
1a) $H^*$
By definition, this is a win for Header regardless of whose turn it is to play.
1b) $T^*$
By definition, this is a win for Tailer regardless of whose turn it is to play.
Two sections of coins
2a) $H^*T^*$
Either player can win by placing their coin as their own piece and flipping the opponent's. For example, Header can win by playing $H$ to make $H^*T^*H$ and then flipping all the $T$s. Tailer can win by playing $T$ to make $TH^*T^*$ and then flipping all the $H$s.
2b) $TT^*HH^*$
This is a winning position for either player since they can flip their opponents coins to win.
2c) $TH^*$
This is a losing position for Header since he cannot flip the first $T$. Any play he makes will result in 1b) - an automatic win for Tailer.
2d) $T^*H$
Losing position for Tailer.
Three sections of coins
3a) $T^*H^*T^*$
An immediate winning position for Tailer by placing $T$ and flipping the $H$s.
This is also a winning position for Header by placing $H$ to make $T^*H^*T^*H$ and flipping the first section of $H$s to leave $T^*H$. By 2d), this is a losing position for Tailer.
3b) $H^*T^*H^*$
This is obviously a winning position for Header.
This is also a winning position for Tailer since he can play $T$ and flip the section of $T$s to leave $TH^*$, which is a losing position for Header by 2c).
Four sections of coins
4a) $HT^*H^*T$
If Header plays an $H$ and then flips any section, he will leave $H^*T^*H^*$, which is a winning position for Tailer.
If Header plays $T$, he will have $HT^*H^*TT$. Flipping the first set of $T$s leaves $H^*T^*$, a winning position for Tailer by 2a). Flipping the middle set of $H$s leave $HT^*$, also a winning position for Tailer by 2a). Flipping the last set of $T$s leaves $HT^*H^*$, which is three sets of coins, proven by 3b) to be a winning position for Tailer.
Thus, this is a losing position for Header.
By symmetry, this is also a losing position for Tailer.
4b) $TH^*T^*H$
If Header plays an $H$ and then flips any section, he will leave either $TT^*HH^*$ or $THH^*$, or $TH^*T^*$. All three are winning positions for Tailer by 2b) or 3a).
If Header plays $T$, he will have $TH^*T^*HT$. Any move will result in three sections of coins, both of which are shown by 3a) and 3b) to be winning positions for whose ever turn it is.
Thus, this is a losing position for Header.
By symmetry, this is also a losing position for Tailer.
4c) $HH^*T^*H^*TT^*$
This is different from 4a) because Header now has the option to flip the first set of $H$s as well. So, if Header plays $H$ and flips the first set of $H$s, he leaves $T^*H^*T^*H$. This is a losing position for Tailer by 4b), thus Header can win with this setup.
Again, by symmetry this s a winning setup for Tailer as well.
4d) $TT^*H^*T^*HH^*$
This is different from 4b) in that Header can also flip the first section of $T$s. If Header plays $T$ and then flips the first section of $T$s, then Tailer will be left with $H^*T^*H^*T$, which we showed in 4a) is a losing position for Tailer.
Thus, this is a winning position for Header.
By symmetry, this is also a winning position for Tailer.
Five sets of coins
This brings us to the initial configuration for Header: $HTHTH$. By playing $T$ and flipping the first $T$, Header will make the set of coins look like $H^*THT$. This is a known losing position for Tailer by 4a).
Thus, Header can win by playing $T$ and flipping the first $T$.