Uh, that doesn't make sense to me. Could you provide some details? The point of SIM card is that there is no user-controlled software in the path between SIM card and antenna. So if the pipe from SIM to antenna was secure before custom ROM, it's still secure after it.
In my e-signature workflow, I initiate the process from outside. So, a network provider notification comes in, I accept it, check a fingerprint presented, enter PIN, and hit send. So, there are couple of screens and a keyboard is presented to me.
When I used a custom ROM, I never received the notification, IIRC. Even carrying the relevant bits from the official ROM didn’t matter. It never worked, crippling tons of things at the end.
If used or reflashed the stock ROM, things have returned to normal.
