WASM is still young. The tooling around it hasn't gained maturity yet. Do you remember trying to debug Javascript before the creation of the in-browser debugger? Desktop application developers back then probably felt the same way you do now.
> this seems like a huge layered mess just waiting to trouble those poor devs.
WASM is a VM. It's less complicated than a javascript engine. How complicated it seems in daily practice is going to come down to how good the tooling is.