sometimes it's not clear what has been updated when I go to a dotted game, might be a new linux/mac version or something not relevant to me.
That strikes me as nothing at all to do with Galaxy. That problem cropped up with the introduction of Mac and Linux support and GOG failing to filter updates by OS. There should be checkboxes in the account settings where you can express which OS(s) you're interested in updates for. This would have been a problem regardless of whether GOG had started bundling Galaxy (optionally) or even if they hadn't developed Galaxy at all.
Aaaanyway, let's get back to discussing the travesty that is GOG passing on Opus Magnum. Personally, I would never buy the game on Steam and I've had enough of Humble's BS (doing things like selling games with a DRM-free download and Steam key and then removing the download). I wish Zach had gone for somewhere like itch.io if he was only going to support one DRM-free store.