> This makes the already complicated module resolution logic in most bundler/packaging tools even more complicated as they must account for the intricacies of another package manager. A house of cards being stacked on another house of cards...

JSR is a registry, not a package manager. npm allows you to add multiple registries and JSR provides an npm API endpoint. From npm's point of view packages coming from JSR are the same as those coming from the npm registry itself. The only difference is where the package is coming from, but all semver resolution, etc are done as usual by whatever package manager you use.

Disclaimer: I wrote a good portion of the npm tarball generation code.