Honestly, I can’t think of a good reason. This is just how email has always worked. What Thunderbird stores locally is identical to message on the server. It’s not decrypted because no conversion happens when syncing mail.
I agree, it would make sense to keep plaintext emails locally or on a trusted server for practical reasons.
This does not answer the question. OP wants to Thunderbird to decrypt PGP mails. Yes, it makes sense to use an encrypting fs, but we are still missing this thunderbird feature.
Nextdns Next DNS is nice when you want customizability.