Yes, AT commands are not unusual. It needs a chance to autobaud which it can't do if it starts to transmitting directly. And the user must be able to turn on/off the radio module and to get feedback if it is connected. Some modules - not all - allows the setting of the PIN code.

It isn't uncommon that AT commands can be used to preconfigure the module so that one GPIO pin requests a connection and another pin reports that it is paired. Then the microcontroller may think it is a normal cable with handshake, so the microcontroller tells it's ready and when it gets the go-ahead from the other side it may just send data.

But the important thing is that the bluetooth modules don't put any special hw requirements on the microcontroller. Some of them are even multi-voltage so they may operate on anything between 3 and 6V making it easy to adapt to the logic levels of the microcontroller.

All this falls out almost immediately by reading the datasheets for a couple of modules. It's always meaningful to google and read up a bit before asking questions on forums. Starting to ask questions with zero preparation is about as silly as asking a forum if it's best to tie the left or right shoe lace first. People will just get irritated, and for a good reason.