Yes, the two sets does affect the probability of finding one match.
Indeed, given a set $A$ of length 5, call $p(A) $ the probability that a random set of length 10 contains $A$. Given two sets $A,B$ we have
$$ p(A \text{ or } B) = p(A) + p(B) - p(A \text{ and } B) $$
The probability $p(A) $ depends on the "shift-symmetries" that $A$ has: the more it is symmetric, the less is probable to find a match.
Example 1: HHHHH can appear in first position in $2^5$ possible combinations, all the ways one can choose the last letters. It can also appear in second position in $2^5$ possible combinations. Continuing like this, it can appear in position up to six, yielding $6*2^5$ possible combinations. But wait..! Actually the first and second block of combinations overlap when the word starts by HHHHHH, so we have counted this combinations twice!
Taking this complication into account, one obtains
$$6* 2^5 - 5* 2^4 + 4* 2^3 ... -1 = 57 < 192 = 6* 2^5 $$
Example 2: if you take THTTT, the first block overlap with the fifth, and the second overlap with the sixth, and that's all. So you will have $6*2^5- 2* 2^4 = 160$, about three times the odds of the word above!
To conclude, the mixed term roughly gets bigger the smaller word you can find containing both of your $A$ and $B$. Let's call the length of the smallest word containing both the "combined rank". This is only a first approximation of how big is the term. Since it has a minus sign, the combined probability gets bigger if the combined rank is high.
Example: $THTTT$ and $HTHHH$ are cool words, because the shortest word containg both is 10 long, and singularly the words have few shift symmetries. Explicitly you get that the possible combinations are $160+160-2 = 318$.
On the other side, if you take $HHHHH$ as first word and $HHHHHH$ as second, this has a very small probability, because they have a lot if shift symmetries and the combined rank is 5. You get $57$ possibilities, way less than above.