BIP141 requires the witness program to be 2-40 bytes for segwit versions 1-16 (for v0 it must be either 20 or 32 bytes).
When would a 2 byte witness program ever make sense?
The 16 bits entropy is nearly non-existent, so it can't make sense for cryptographic purposes.
I can come up with some possibly silly suggestions, wild handwaving:
- The usefulness of 2 byte witness program is unknown at present time, but BIP141 doesn't want to unnecessarily close doors. It might prove useful in the future.
- Use it as some kind of 0 value OP_RETURN but the data is stored in the witness of the spending transaction.
- A certain witness version and a two byte witness program, for example 0x52020000, on a 0 value output activates some new rules for encoding outputs, possibly to enable sub-sat amounts, or some fancy privacy feature. The actual output is attached elsewhere in a similar fashion as in segwit.
- Use it as an "exodus" address to recreate all spent UTXOs to another system external to Bitcoin.