Having a separate isolate in each threads spawned with the worker threads with a minimal footprint of 10MB does not seem like a high price to pay. It's not like you're going to spawn hundreds of them anyway is it? You will very likely spawn less or as much threads as your CPU cores can handle concurrently. You typically don't run a hundred of threads (OS threads) you use a thread pool and you cap the concurrency by setting a limit of maximum threads to spawn.
This is also how goroutines work under the hood, they are "green threads", an abstraction that operate on top of a much small OS thread pool.
Worker threads have constraints but most of them are intentional, and in many cases desirable.
I’d also add that SharedArrayBuffer doesn’t limit you to “shared counters or coordination primitives”. It’s just raw memory, you could store structured data in it using your own memory layout. There are libraries out there that implement higher-level data structures this way already