Is it correct that Glyphs will define many custom parameter values by its own (if they are not set manually), like fsType, panose or vertical metrics? If so, is there a way to find out which parameters and which values Glyphs will set?
Glyphs will not set the values, MakeOTF does. You can check what Glyphs will put into the font by checking the feature.fea file in the temp folder.
ah, ok. Great, thanks!