Are there any differences between Skyrim & Skyrim: Special Edition

From the Ms. Pac-Man Wiki page:

The ghosts' behavior patterns are different and include semi-random movement, precluding the use of patterns to beat each level.

The page also mentions a few other changes to game mechanics, such as the fruit that now moves and multiple mazes, although there is nothing to suggest that the player control was changed.

From the same page:

The Mega Drive/Genesis, Master System, and NES versions, by Tengen, and the Super NES version, by Williams Electronics, took a few liberties.

Based on this information you should not expect Ms. Pac-Man to behave the same as the classic arcade Pac-Man.

The two files simply store different things. The Skyrim.ini tends to be a little bit more core to the game - memory tweaks, the uGrids setting, etc - while the SkyrimPrefs.ini is more for things that are actually likely to changed by most users (not directly, but the launcher/in-game settings edit this file so this is basically the preferences store).

In practice, if you have a specific tweak you're trying to implement it will belong in one of the two files, put in the other file it will likely have no or an unexpected effect. Most of the tweaks that are safe and easy belong to SkyrimPrefs.ini.

Also, do note that there are plenty of new items you can add to the two files, so if you're trying to improve performance make sure that you go and look up some tweak guides that will give you these extra items to add. Tweaking what is already in the files won't cover everything.

Oh, and make sure you edit the ones in My Documents\My Games\Skyrim and not those in the game's install directories.