I'm interested in doing IL runs on a PC copy, but I also want to mess with the game files to let me use SWBFspy servers in case I want to do multiplayer. Because it's technically a mod, would it invalidate a run?
No, it's a legit run. The SWBFspy exe runs 1.2 and the files included in the downgrade I showed you are the stock 1.2 files (shell.lvl and common.lvl). You can actually check the dates on those two files as well (12/2004 iirc) but the only difference between the steam version is the menu code. Except for the replacement of gamespy strings, it is the same as the release version of 1.2 and does not have any differences in difficulty or RNG.
We allow runs on 1.0/1.1/1.2/1.3 (steam version), however, 1.2 and 1.3(Steam) are definitely the most prevalent, other than console.