Tried the tool last night and have a unique problem.
I have three Elite installs, one for each account. Two Frontier, one Steam. The tool only picks up one and does not let me add the others. I can run the launcher independently, but would be nice to choose accounts as I do not use VR for my main account for exploration.
Also, if I use the tool and keep it active after changing the settings (1920x1080, fullscreen for Vive) then start E: D, the screen still reverts to windowed 1280 x 720 on game launch. That non-persistent screen settings in VR are a bug and has been reported, but FYI.
You can change which Launcher it is "launching" by going to My Documents\EDProfiler\Defaults and changing the "Launcher" path to the one you want. I don't think I'll add the functionality to have different ones, it's a bit to niche and messy
And yeah, it seems that the game changes the setting, nothing can be done. Hopefully they will fix the bug