Javelin anti cheat question

Hello! 
I havent launched 2042 in a long time and wanted to jump in after seeing bf6 footage. I just discovered that theres a new anti cheat and there seem to be lots of ppl having issues. I use cheat engine to run Spartan Mod for Ghost Recon Breakpoint along with mods and nexus's mod manager for many single player games. Will the new anti cheat do anything to my system if these apps are not running or when I run them while not in BF? Im just concerned having them may lead to issues, which my friend says it will, so I would like to be sure before reinstalling. Any help would be appreciated. 
Thanks