You can specify a top level folder of where all your mods get installed. Then, off of that root, it'll install the mods in a non-conflicting way. This design consideration was made so people wouldn't get stumped on folder names.
So if you picked D:\7D2D, then Spider's True Survival would be installed under D:\7D2D\Spider\TrueSurvivalSDX. You can pick the top level, but not where the individual games go.
When you say pick a folder, are you referring to the top level folder, D:\7D2D in the above example? Or did you want more specific control over where, let's say, True Survival SDX gets installed?
The 7D2DModLauncher.exe can be placed anywhere, and can be added to Steam as a non-Steam game to enable the overlay.
Unfortunately, due to the installer I use, the Mod Launcher itself gets installed as a One-Click application, so we don't get to pick where it goes. I don't even have that level of control; it's strictly a Microsoft decision.