> That breaks if the library uses build scripts

Uh… no.

> setting up native binaries, or native modules linked against the specific Node version

So the majority of projects—those that don't use binary NodeJS modules—don't have a reason for sidestepping the primary VCS and going along with npm's shoddily designed overlay version control approach?

> However, I would just stick with regular pnpm and installs.

You're not answering the question. npm isn't bedrock, and pnpm certainly isn't. If you're going to introduce (mandate) the use of a tool in the workflow, you should be able to justify it by explaining your rationale for introducing it (and making everyone deal with the associated costs). You should at minimum be able to provide a lucid explanation of the tradeoffs. For good measure, you should be able to disprove the "NPM Null Hypothesis"; you should be able to state a straightforward answer to the question, "What problem is this supposed to be solving?"