Yes, that's correct.
The MSV-2 module which talks to the CPU directly is just a glorified (and expensive) EEPROM programmer. You can do the same thing with an EEPROM programmer that will talk to the motorola MCU chip that is used in the BECM, however the difference with the Faultmate is that you get the nice user interface with check boxes for all the settings, whereas an EEPROM programmer will just give you a full dump of what's stored in there - which is no used to anyone unless you know what memory addresses and the formats all of the information is stored in. I sat down over a couple of evenings a month or so ago and have worked out how all the relevant vehicle information, settings, and even the lockout status is stored as I was interested in how it did it.
The BECM alarm lockout is one HEX byte, and luckily if it's alarmed, then even if it shows up as garbled information on normal diagnostics - all the vehicle information is retained, and when the alarm lockout is reset you don't need to reprogram anything else. Just write the alarm lockout and EKA lockout statuses back to 'Normal', and refit to the vehicle. I usually ask owners for VIN, EKA, mileage info aswell to cross reference that against what's stored as occasionally I've seen the EKA corrupted.