PEP-484 is still provisional, its API may change. The parser comes from the [Universal Ctags](https://github.com/universal-ctags/ctags) project. The latest version of that appears to support PEP 526 annotations, but not PEP 484.
Updating parsers in Geany is "in progress" but is a big job and somewhat slow, but when complete those PEP526 annotations should not break the parser.
You should open an issue with the Universal Ctags project to discuss adding the full PEP 484, perhaps when it is finalised.