Let me see if I can explain "why" to you. The PS3 steam upgrade kit uses the PS-32 stacker board set and what is essential PS2 basic steam wiring (no MUX) and thus no special features in the engine side of the harness. They have you reuse the existing constant voltage lighting board in the engine. All this is again, because of 2 reasons, the wiring harness is the 10 pin tether which limits how many features can be accessed (turned on and off or controlled- like marker lights, number board lights, cab lights, firebox glow) inside the engine. You get none of that from "the kit" because there simply are not enough wires in the 10 pin tether for all those features, plus the required ones like the tachometer for speed control, power for the motor, independent smoke fan and heater. So basically, you get one "controlled lighting feature"- headlight . Again, there are 2 things kind of driving this, the PS2 compatible from a wiring and output standpoint of the PS32 stacker board set, and then on top of that, your wiring harness in the kit is designed around basic steam features- sans the addition features that could be done in production PS2 engines that had the MUX transmit and receive boards respectively.
So what is key here is the MTH file system consists of 2 parts, one is called chain files and that is the firmware or function of the engine. I could go into why it's called chain files has to do with making the files by linking snippets of machine language code that make up the files. Again, chain files are a zip of multiple files that make up the firmware if you will of the board to implement the functions and features. You most likely will not want or need to change this and doing so could make your board set not function since it is a PS32 stacker set.
Conversely, the *.mth file is the sound file. Now just a note, sound files are technically not just sound files, they also contain feature programming info so that when you add the engine to a DCS control system (remote or app) those buttons and features show up and can be controlled. Again, just suffice it to say, the sound file also is not just sounds, it contains settings.
So what you need to do is neither of that you listed. You need to go back to the page for the original engine. https://mthtrains.com/20-3028-1
On the support tab there is the upgrade sound file only.
You want to load that sound upgrade file.
"p04_pp3blucometall040707a_3v.mth" that I also attached here while I was inspecting the file for suitability.
"So do I use the PS3 or PS2 sound file? There's one of each on MTH's website, one for the PS2 20-3255-1, and one for the PS3 20-3461-1."
If you use the other files, I think you would run into problems. The newer PS2 file I know for a fact that engine has the MUX boards to allow for more lighting features. You have no MUX. The PS3 file is for a direct modern PS3 2 board (boiler board and tender board) system with wireless tether and that's also not what you have and in theory would be problematic.