This is the bread-and-butter of what Linux distributions do. A large number of larger software are slightly altered in order to integrate this or fix that, but they are close enough to the original that there's little confusion in practice that e.g. Debian's Mesa is still Mesa, and Debian's kernel is still Linux, despite alterations.
Is it very different than the Linux kernel? There are thousands of custom versions, old versions, and strange architectures and they're all called "Linux" and it's worked fine so far. Some organizations even backport security fixes without changing the version number. As long as you're clear about what you're doing, why is this any more confusing?
The word “Linux” no longer has a singular meaning. And distributions have their own branding.
If someone wants to release DebianRust and DebianCargo that would be perfectly fine and non-confusing. A distribution could also make an agreement to use the Rust/Cargo trademark under some mutually agreeable terms. Likely having to do with no major changes and staying updated.
Most Linux distributions apply patches to software they distribute (e.g. for integration or security fixes). That is expected. If trademark forbids that, then it adds problems and confusion (like Firefox renamed to Iceweasel in Debian, until they reached some agreement with Mozilla Foundation).
It still does the same thing, but now in a non-general, distro-specific way. Hundreds of distributions customize their software like that: for example, I believe it is actually more common to find gnome-terminal with patched-in transparency than the vanilla one without it.