I'm the dev for the interface scaling mod. Essentially the way the UI was designed it was not meant to work on non-4:3 or 16:9 screens (if scaled). They designed all the interfaces for 720p and 4:3 (as this is what Xbox supported).
On PC you can bump it to 1080 and nothing scales, but it is still passable. At higher resolutions their lack of scaling obviously does not work. They did not implement code to deal with scaling nor non-standard aspect ratios.
I added in scaling (so it will scale up to what it would be like at 720p) but there is little flexibility in the interface. Writing code for aspect ratios would be awful to write and requires more resources than I can provide (there are a lot of interface files).
Additionally there are no "Trojans" in Mod Manager. The whole thing is open source, you can build it yourself even. Some of the included files have to modify game processes so mods work, that's part of modding the game. The files are relatively new on the latest releases because they were freshly compiled. Lots of AV programs like to flag newly built files that don't have a reputation yet. I'm not going to fork over thousands for a code signing key.
