(Spoilers for ruin) Theory

My theory on prototype freddy

It’s obvious that prototype freddy isn’t the one in the main game, and since the Princess quest ending is confirmed canon (freddy left his body at the pizzaplex.) they used the freddy casing and made a new Glamrock freddy but since they didn’t have the casing for the head it remained incomplete therefore a prototype. This is further evidenced by the fact it has a present in the chest like the original did which contained the fazwatch which you cannot see in the original freddy after collected. This is all just a theory however.