you can generally use certificates, but those certificates generate a sort of PGP Wrapper Key after importing to PGP Desktop , so this wrapper key/pair based on pgp-keypair is then used to encrypt the folder/file via File/NetShare .
i dont tried smartcard/token with FileShare so im not 100% sure how the key-saving to the token works. good idea cause i remember i wanted to talk with a SE from Symantec about this topic so i can share ideas after i spoke with him .
so to summarize generally : from my understanding only certificates can be saved to tokens/smartcards, and from my understanding each time you import your p12/pfx certificate to PGP desktop a "new" pgp wrapper keypair is generated having another fingerprint and also other expire date based upon importing the key, so it's normal that a new fingerprint and keyID is generated. but the decryption works smooth and the fileshare folder still can be accessed.
perhaps someone of the smartcard/token fileshare users could point it out how it works regarding "workflow" if you use tokens/smartcards with your certficiate to encrypt folders.
thanks!
ben