However, most longs are just numbers that have no metadata. I guess you'd set the metadata portion to all zeroes in that case. This feels like a reified version of Rust's pointer provenance, and I think you would have to expose some metadata-aware operations to the user. In which case, you're inviting some code rewrites anyway.
While not as bad as the register/ALU ops issue, you're still making all code pay a storage size penalty, and still adding some overhead to handle the metadata propagating through arithmetic operations, just to accommodate bad code, plus it complicates alignment and FFI.
And yes, there would still be some overhead for storing and propagating the metadata, and struct alignment would change and FFI wouldn't work with longs.