According to my knowledge Godot can’t reuse one WASM runtime for different PCKs, so each game has to start its own engine, which causes the short freeze. The best you can do is reduce the cost:
Preload the WASM when your SPA starts so it’s already compiled.
Keep a single iframe or canvas alive instead of re-mounting it.
Use a minimal custom web build (no threads, no 3D) and let the browser cache it.
This won’t remove the stall completely, but it keeps it about as low as Godot allows today.