MH regional flights (including Phuket) use the main terminal and their domestic flights (Penang) also use the main terminal. As such, you do not have to use the aerotrain to transfer between terminals.

There are special immigration counters for those transferring between international and domestic flights, where you don't have to go landside. Usually there is hardly any queue at these counters. 1hr is a very comfortable transfer time unless your incoming flight is delayed.

If you have not paid for your ticket, it's worth looking at Firefly which I believe still fly direct from HKT to PEN using ATR70.