It involves fiddling the database header to ensure you can keep track of the read-set from the VFS layer, by convincing SQLite to drop its page cache at the start of every transaction.
Other than that, a MVCC VFS is relatively straightforward. Here's an in-memory experiment if a few hundred lines of Go: https://github.com/ncruces/go-sqlite3/blob/v0.29.0/vfs/mvcc/...
I haven't settled on what's a good storage layer for something like this.