The funny thing is that the performance of a 12MB WASM blob is probably superior to most Shiny apps with more than light traffic.

Usually they are shipped in a compressed form. If 12MB is compressed it could be that it represents the entire R runtime to support the general R REPL. It could be possible to reduce the payload by compiling only what's necessary to run a particular R program into the wasm binary. That should cut down size considerably.