Have you spent much time on JSR yet?
Even for Node projects I've started searching JSR first and comparing JSR scores of libraries. If a project advertises first-class JSR support now, I pay more attention.
The compatibility layer works in both directions here. JSR is a fascinating growing home of Typescript-first, typedocs everywhere, ESM-native ecosystem. Most of those install just as well into Node as Deno (though they are easier to use in Deno, by far). I want Typescript-first. I want ESM-native. I have a registry now that gives me some indicator if and how much a package author cares about those things.
The compatibility layer didn't remove the incentive for Deno (the Company) to help create a JS ecosystem that isn't just layers of garbage dependencies piled into trenchcoats, the compatibility layer encouraged Deno to expand their horizons and make Node better too by providing a Registry like JSR. I think JSR is a better way to promote a new, fresher JS ecosystem (for all) than restricting what sorts of packages are compatible with the Deno runtime. It's got gamified test scores! It's got provenance data and supply chain transparency!
If they hadn't added the compatibility layer to Deno too many people would have chicken-and-egg excuses that all the packages they need are in npm and never even tried Deno. With the compatibility layer in place Deno gets to shine in its own place of what it can do better than Node, then suggest you try JSR in all your hobby projects, then get you using JSR even in Production on Node packages until it is even easier to convince your day job to switch to Deno for better performance and increased security and deep OpenTelemetry support… Deno's still helping a lot to create a new JS ecosystem with fewer layers of garbage, compatibility or not with the old layers of garbage.