I think you can analogize these server JS runtimes (Node, Deno) to browser runtimes (V8, JavaScriptCore, SpiderMonkey) and to the APIs that ship with those. When one browser JS engine invents and exposes a novel feature + API surface for it that the other engines don't, what happens?
If there's any demand at all for doing what the feature does, then devs will tend to write polyfills to make the feature "work" (for some value of "work") in the other engines, so that their code can still be "portable" (i.e. at least not crash) despite calling the feature. Also, eventually, the other engines might introduce their own versions of the feature, with their own APIs, for the polyfill to fill over; and then even more eventually, those will get standardized.
If there's a huge demand for the feature (think: XMLHTTPRequest), then other engines will rush to just clone the feature's API as-is, so that their engine won't be held back by the lack of it, or by the bad performance of a polyfill solution.
But if there's next-to-no demand for doing what the feature does, such that you can predict that nobody will even bother to write a polyfill, let alone port the feature, and so the feature will languish in that one engine — then yes, people will intentionally avoid using that feature at that point. See e.g. most of the Microsoft ActiveX-based stuff you could do in Chakra (IE's long-dead JavaScript engine.)