I think you can stress physically with the words in either order:
1a. Though not very physically attractive, [...]
1b. Though not very attractive physically, [...]
But you can only stress attractive in the final position:
Though not very attractive physically, [...]
2b. Though not very physically attractive, [...]
Example 2a sounds unnatural, so it's an unlikely reading. But although example 2b sounds possible, it's a reading that is contradicted by the rest of the sentence:
[...] she possessed a good sense of humour.
Unfortunately, the reader doesn't know that 2b is an incorrect reading until they read the rest of the sentence, so it's possible they may begin reading with the wrong stress pattern, then have to backtrack and re-read the sentence once they realize their mistake.
To avoid making the reader do that extra work, you can choose the sentence order that forces the stress onto physically, which is unambiguous:
Though not very attractive physically, she possessed a good sense of humor.
Of course, this problem only presents itself in writing. In speech, the intonation would be unambiguous.
Alternatively, you can solve the problem by indicating stress with italics or bold, as I did in the examples above. That prevents the ambiguity regardless of word order.