I don't remember it by heart. But basically, TSN-SOM is playing the super-advanced game (with possible double stealings, runners advancing on throws, and so on), but several advanced options (like weather effects, special plays, etc )are not on.
One option I know for sure that TSN-SOM turned off is the homerun normalization----in the computer game (I can't tell if you can turn this option off, or if it's automatically on), if B.Roberts (to take one player as an example) is heading towards 100 homeruns after a quarter of season, then SOM will cool him off to make sure he hits a "reasonable" number of homeruns. To repeat, this option is off in TSN-SOM, but I believe that it remained on for other things like strikeouts, doubles, and perhaps triples as well (TSN didn't give the specifics, but only said that it was convinced by SOM to maintain the normalization for a few statistics, without detailling those statistics).
Pitching wise, I believe that TSN uses slightly different fatigue rules with relievers, such that overusing relievers in TSN will cause relievers to be worse than in SOM.