You are absolutely right, these can be confusing to somebody not familiar with Dreamcast discs or with TOSEC naming scheme.
Here's an explanation...
Starting with the (M3), (M4), (M5) after the country: these are flags indicating the number of languages supported by the game. So they actually mean Multilanguage 3 etc etc. This is defined by
our naming convention:
In cases of more than two languages or countries being required, (Mx) is used to represent multiple languages, where x is the number of languages:
For example: (M3) for 3 languages, so "Legend of TOSEC, The (1986)(Devstudio)(M3)"
For example: (M4) for 4 languages, so "Legend of TOSEC, The (1986)(Devstudio)(M4)"
Sadly this naming method doesn't tell you which languages they are, but I still have to follow existing rules when naming the file. The most usual languages will be English, French, German, Spanish and Italian, althought there are several exceptions to this!
The [xS] or other similar [more info] flags at the end of the filename, differentiate between different print runs of the game.
Without getting too technical, when a disc printing factory reprints the same disc, usually audio tracks become slightly shifted (and hence have different checksums when dumped). The ringcode (also called mastering code) is a sequence of numbers that are like a coded identification of the disc. Discs from the same factory and of the same print run, have the same ringcode.
For example, we currently know 3 different print runs of the USA version of The House of the Dead, with ringcodes *9S* 51002, *12S* 51002, *13S* 51002
The shortest way you can differentiate between them is using the 9S, 12S, 13S part of the ringcode. That's what you see in the filename, a part of the ringcode that uniquely identifies a disc.
Same thing happens for other discs that came from this factory, like some in your examples.
The good thing is, these variances are minor from a user's point of view. The audio tracks are basically the same and the shift of audio data is just a few milliseconds. So a human can't hear the difference. But of course the computer knows it's there and we need a way to show the different dumps/print runs in our dats.

For NFL 2K, things become more complicated.
Obviously due to popularity, game was printed in many print runs and in 2 different manufacturing plants. One of the factories uses the *xS* coding and the other uses MT Bxx coding.
So we currently know these ringcodes for this game:
610-7895-0444 MT B08
610-7895-0444 MT B13
610-7895-0444 MT B19
610-7895-0444 MT B20
*9S* 51003
*10S* 51003
*10S* 51003
*11S* 51003
*13S* 51003
All *xS* dumps are different between them and different from the MT Bxx dumps. BUT the MT Bxx dumps are identical for all the discs. So the simplest way to indicate that with as few additional filename characters as possible, is to use all the MT Bxx parts bundled together. And confuse users in the process...

Hope things are a little clearer now...