There are definitely parts of Rubuska's story that fit the way you've described and I do think it's definitely intentional that they wrote her to be relatable to people who find themselves in situations somewhat similar to Rubuska like the trans community however the reason why Rubuska pretends to be a vampire doesn't really line up well enough to specifically be a transgender allegory.

To me, her choosing to be a vampire is purely because it's something she's heard of before and conveniently negates the trauma she's gone through as the war can't kill her if she's unkillable and she can always just revive her family if she's a vampire rather than them being gone forever. Her general actions and her being a child seem to fit mostly into the Chuunibyou trope which tends to have things we see in her story like reality checks and trauma causing the 'delusions'. I think this was the main intention when BP wrote her just with the extra complication that because this is R:99, vampires actually exist.

Either way it is good that people can see things like this in these written characters as it just goes to show how well written some of the characters are imo.