I just did a quick check and yeah I was wrong: the occurrence of the missing flags is definitely lower than I thought. But I have done a check of past releases on Prime for you in case you or anyone else is interested. I might have missed some because I already owned store copies of them, but anyways here's Prime-obtained games which aren't flagged as "In Library" for me:

Fallout: New Vegas Ultimate Edition
The Elder Scrolls III: Morrowind GOTY Edition
Neverwinter Nights: Enhanced Edition
Doom 3
Greedfall
Mafia II: Definitive Edition
Bioshock: Remastered
Bioshock II: Remastered
Tomb Raider: The Last Revelation + Chronicles
Blade of Darkness
Quake II
Syberia: The World Before
Gamedec Definitive Edition

But when checking for true ownership I always use the orders & settings or my library list via browser. The store isn't perfect at marking ownership, and often gets confused if you own a "definitive" edition but doesn't mark other included lesser products as owned at the same time. It's actually a bit of a mess.

Thanks for the extra info. Yeah, I must have overlooked this until now, I already owned a bunch of those, but Greedfall is missing too. I had been verifyin code redemption by checking my library before, it wasn't until about a month ago that I noticed the store showing prices for some redeemed games.

The inconsistency in displayed ownership is confusing. Hopefully GOG gets that figured out some day.