The way I bundle into SEA is modules that need to be imported from disk (that can't be bundled due to node or wasm modules), is just include them in the assets, and do a "write to tmp, import, delete" flow. It works.
Not saying vfs is bad, just it's not impossible in a few lines of code to set up that. My idea for a simple version of a vfs in node is to use a RAM disk/RAMfs - would that work?