There are a few additional files that you are welcome to modify to your personal tastes (that is, it will not modify game balance in any way). I encourage you to avoid making any changes that would alter gameplay in any of the files, but I'm not your dad, so do what you want.

Here is a list of .ini's that I have curated specifically for Synthesis, and as such, I discourage you from changing:
-PlugY.ini
-SEO.ini
-D2Mod.ini

Please be aware that modifying these .ini's is NOT supported and, at worst, might brick your character irreparably. At best, it's likely to be considered a cheat (I mean let's be real, would 10 skill points per level balanced???).

It is highly encouraged that you modify resolution and autopickup/drop notifications to your personal tastes.
Resolution options can be found in d2gl.ini; if you don't want to use d2gl, you are welcome to, but I won't support those changes. I will say, however, a number of users are using sgd2freeres just fine without d2gl. It should be an easy swap if you choose to use another resolution utility, just follow those directions (and delete all d2gl files). Note that pressing ctrl+o in-game will bring up the d2gl options, and there are a lot of them there that will allow you to tailor your graphics experience. I've included my personal preferences with the mod, but any changes you make will be automatically saved, so feel free to mess with things.

Autopickup and drop notifications share a lot of similarity so I will discuss them together. In the d2tweaks.ini file, there are sections for autopickup and drop notifications, and you are able to add any item types (4 characters), or item codes (3 characters) to these lists. As expected, autopickup items will be automatically picked up as you walk over them. Drop notification items will show a message in the "game chat" and in my experience has about a full screen range. Both autopickup and drop notifications have a number of lists available which can be populated with items however you'd like.

For these item lists, please refer to the standard LOD item codes and types for base game items, and the NEW ITEMTYPES AND ITEMCODES.txt file bundled with the mod for most of the items added in Synthesis.

There is another .ini file that controls the key to enable/disable the toggle functionality of "show items", D2Alt.ini. Note that this does not change the key to actually show/hide items, it is only the key to toggle between the PoE-style functionality and the vanilla D2 functionality.

Again, ANY changes outside of the ones listed here are NOT supported and I strongly discourage you from messing with files.