When Node first released its biggest selling point was being able to reuse web APIs. It also filled in gaps for APIs that weren't standard in browsers. Then browsers started to add these APIs, and some of Node's implementations naturally diverged (aka the idiosyncrasies that you mention).
Deno has the advantage that they are starting from a clean slate without the burden of legacy APIs, but how long will that hold for?
Deno has the advantage that they are starting from a clean slate without the burden of legacy APIs, but how long will that hold for?