Of note is that the Trezor Safe 5 still has the card slot to use SD Protect even though it contains a SE. Wouldn't hurt to continue using SD Protect along with the SE, but maybe that is overkill. We all have to decide for ourselves.
I see no reason not to use it just because the device has a secure element. It's extra protection against physical attacks. If you don't have the feature activated and someone knew your PIN, they could get access to the crypto you stored there (assuming there is no passphrase and/or they don't know it). If you do have SD protect, the knowledge of the PIN wouldn't help if the person also didn't have the MicroSD card. It's physical 2FA.
Btw, does Trezor have an official name for the feature? I am pretty sure it isn't 'SD Protect.' I started referring to it that way, seeing your recent posts. Isn't it something like 'PIN Protection' or 'PIN Encryption?'