There have been ideas both ways.
One way is as you mentioned, all transactions keep the same default fee to ensure maximum fungibility in the shielded pool. But the issue there is the default fee is so cheap it makes it trivial cost to issue/use a ZSA token.
In my opinion there should be a higher fee for ZSAs because they are using Zcashs blockspace for something other than transacting directly with Zcash:
But the key to maintaining fungibility in that scenario would be for all ZSAs to use the same higher fee.
Yes, it’s a trade off in that looking at just fees on the chain a Tx could be attributed to “some ZSA transaction took place” vs “some regular Zcash transaction took place” but it would need further study to know if it’s worth the trade off.
To me it seems like a good compromise if it makes ZSAs “consume” more real Zcash to operate.