Star Trek Transporters don’t annihilate you. According to all the stuff from Star Trek it literally disassembles you, moves your particles through space in a matter stream held in a containment field, and reassembles you at the new location.

So the Ship of Theseus question doesn’t actually apply, your physical material is the same before and after. The question is if disassembly constitutes dying, and if the reassembled you at the new location is a resurrected you, or if disassembly isn’t dying, then it is in fact just a form of transport.