Hmm. Okay, digging around in the Yarn repo, I see this "generate patch" setup code [0]. Looks like they're trying to cherry-pick some specific commits from the TS repo based on the TS version, and specifically apply them to the TS file.
The "base64" bit is referenced here [1].
I would assume this specifically relates to the fact that TS does not have native support for Yarn PnP as a filesystem approach. The Yarn team has been keeping an open PR against TS [2] and trying to convince the TS maintainers to merge it, but it hasn't happened yet.
A bit odd, and I can understand why you're concerned, but it also looks like there's a very understandable reason for this.
I would have assumed that this doesn't get applied if you install TypeScript via the Yarn v2 `node_modules` linker, but would have to try it out and actually see.
[0] https://github.com/yarnpkg/berry/blob/f384f0f40e87d636e4021b...
[1] https://github.com/yarnpkg/berry/blob/f384f0f40e87d636e4021b...