I checked everything in detail a few months ago and even contacted Steam Support, but they weren't much help besides mentioning the profile features limited game might have something to do with it (and something along the phrase "we can't help you any further"). They referred me to the Steam Beta Client discussions, where i explained the issue in detail, but until now there has been no response. At that time iirc the achievement showcase did include the game in the amount of Perfect Games, but the 20 achievements from Gravitas were excluded from the total amount of achievements.

The guide you mention says "Avg. Game Completion Rate is an average of all your individual games' percentages of unlocked achievements". That would perfectly explain the issue. I think what happens is: The Achievement Showcase counted 151 completed games at that time (including Gravitas), but it didn't count Gravitas' achievements. So 150 games at 100% + 1 game at 0% averages at 99% completion rate.

Oof, one can then only hope that the devs will either fix or remove those, otherwise you're cooked. I usually check achievement websites before i start any game, trying to avoid starting a game with broken achievs.