Keystone, It may not make sense at a glance for MTH numbering. Your example of identifying proto 1, 2, and 3 wouldn't tell the whole story anyways. There are three different versions of Proto 2 that I know of... 5 volt, 3 volt 1 meg, and 3 volt 2 meg boards. It may not matter to some, but that is huge to me. What's in the engines is labeled right on the box near the part numbers anyways. You don't see the part number on the engine!
The earliest stuff didn't use the same numbering system and had the MTH/QSI sound boards inside that led to proto 1 I believe.
The modern prefixes are as posted above by Oman. Like 10=tinplate, 20= premier, 30 RK, (40,50,60,track and power stuff) 70=G, 80&81= HO
The suffixes (for engines ) are -0,1,2,3,4,5 that I know of.
-0 is Loco-sound as you suggest. Powered but not command. Just bell and whistle.
-1 is hi rail.
-2 is scale wheeled
-3 is dummy
-4 is certain trailing units sold separately?
-5 is for Marklin AC only in HO?
4 & 5 I'm not sure of because I've never bought them.
You can judge what's in MTH fairly close by the year it was made. The part numbers for 5volt PS3 are usually low and made starting somewhere around 2000?. I believe (around) 2003 was a split year where proto 2 3 volt was introduced.
Barry B, and Marty F. did a post of the years for PS2 2meg releases and all of this.
The latest PS3's are usually in numbers with an extra middle digit. Made after maybe 2012 or 2013 ...14?