Here's something notable about Nuclear Throne, from its original release newspost:
"PLEASE NOTE: Daily and Weekly challenges are NOT available in the current version of the game but will be added in the future."
That was January 11, 2016. Nearly three years later, still not added. So not only is this a case of the GOG version being inferior, but it was falsely advertised in its release news post. That news post also claimed that a Linux version was on the way, which also never showed up here:
"Nuclear Throne, a wild roguelike where you mutate your way to the throne of a post-apocalyptic world, is available now DRM-free on GOG.com for Windows and Mac (with a Linux version also on its way)."
Fun Fact: Cluster Truck originally mentioned the level editor and replay system (both of which are missing from the GOG version) in its GOG store page description, and despite eventually removing that part of the description GOG never even tried to reimburse users who bought the game when the store page had contained that false advertising.
Screenshot of Nuclear Throne release post: https://i.imgur.com/vbPEZZJ.png
Screenshot of original Cluster Truck store page: https://i.imgur.com/J8IR465.png
EDIT: The bit about Nuclear Throne getting daily and weekly challenges added in the future is also still on the store page for it, so more false advertising "fun" there: https://i.imgur.com/WCg888M.png