First of all: this launcher/manager is awesome!
Thanks!

After initial setup, my pilot files weren't copied, in case anyone has this problem, you need to copy/move them to "%appdata%\HardLightProductions\FreespaceOpen\data\players"
Yeah, wxLauncher is the only launcher that does this correctly right now. Since Knossos was designed for 3.8.0, I never took into account that someone might be coming to Knossos from an older FSO version.
Another thing I noticed is the launcher copies retail VPs to its own folder structure, after this, retail installation directory is no longer needed, maybe add a opt-in checkbox to delete the folder (better yet, use Freespace2 as the default Knossos data dir). Opt-in in case someone still wants to play retail via the original exe.
We're currently improving the first time setup. I might add a checkbox to delete the old folder and a notice that it's no longer needed. Knossos can't use the old Freespace2 folder itself since the retail files need to be in a subfolder to work and I don't want to break any existing retail installations.
About folder structure, I observed 'retail' FS2 on the launcher is just calling FSOpen executable with -mod FS2 cmdline, so the retail vps are used as a mod instead. However, other mods are subfolders of FS2, maybe you could make it in such a way that every mod has its own folder alongside FS2 folder. (probs adding ',FS2' to mod cmdline)
That might be possible... not sure. However, the main reason for the FS2 folder is Knossos' TC support. Each TC has its own folder inside the data folder containing the TC files and the mods for that TC. FS2 is treated as just another TC since that was the easiest way to implement TCs. If I moved the FS2 mods outside the FS2 folder, it wouldn't be clear whether those are TCs or mods.
Report button on mod detail screen just 'doesn't work' without a nebula account saved, opens a message box saying: "Request failed. Please contact ngld.", log says:
[...]
Probably it should state the reason it fails is this, or better yet report them without needing an account.
Yes, I'll fix that in the next release. Not sure if I'm going to drop the account requirement since I want to avoid spam (and without the account there's no way I could reply).
Which brings me to the reason of the report: MVP 3.8.2 seems like having a checksum mismatch, whenever I "Verify file integrity", packages MV_Music and MV_RadarIcons show as invalid, despite being redownloaded via Knossos.
That's a result of certain bug fixes on the server... I fixed the downloads but forgot about the checksums. Thanks for the reminder!