Is GOG ever going to show transparency about this?
I've said this before but GoG will never and should never become more transparent about their decisions. If they have issues, that is a discussion between them and the developers and that is private between both parties. Revealing any of that to the public is just not that professional a thing to do. With modern day Twitter lynch mobs and stories running rampant with the "facts" evolving every second, it doesn't serve either party's best interest.
That being said...
From all appearances, Opus Magnum was a solid miss by GoG. Using SteamSpy estimates of ownership and even ignoring the 28,000 Early Access owners, it has sold about 26,000 copies on Steam in just 3 weeks with only a 10% discount. If GoG gets about 10% of those sales (which is probably a low estimate for their share of sales), they've given up 2,600 copies sold.
Those numbers are very solid for an unbundled game with only a small discount.
So barring technical difficulties adapting the game to be DRM-free or adapting to Galaxy from Steam Workshop as the main reason for it's exclusion, the numbers seem more than enough to deserve a place in the catalog.
I shouldn't even have to mention the success of the other games by this developer...
Leaves me baffled as well.