git bundles have a standardised format (defined in [1]) while git archives did not and continue to not have one. Git can still handle all previous bundle versions and you can specify which version of the bundle standard you want to use when creating bundles.
So no the git 2.38 issue should not be a problem for bundles even if the format changes in the future.
Standardized format != guaranteed reproducible. Git makes no promises that it'll keep PACK contents stable, just that they're guaranteed to "deflate" to the same contents.
Which is what the linked article discovered. Threading is a trivial way to discover this, but there's other ways PACK contents might differ across versions.
So no the git 2.38 issue should not be a problem for bundles even if the format changes in the future.
1. https://git-scm.com/docs/gitformat-bundle