You differentiate a Taproot scriptPubKey and a P2WSH scriptPubKey by their witness version. 1 for Taproot, 0 for P2WSH.
A "P2WSH with version 1" doesn't exist, it would just be treated as a Taproot scriptPubKey by upgraded nodes and as an anyone-can-spend by legacy ones.
P2WSH: <0> <32-bytes push>
Taproot: <1> <32-bytes push>...