The reason for that is exactly what you said in the original post: Your sysnand doesn't have the game installed. It doesn't exist in the console's application records there, so the system defaults to the ? icon. The only way to really fix it would be to import the title to the application records if it doesn't exist there already, but that's where stuff starts getting messy and I wouldn't want to risk it, if that makes sense? Even if the game isn't pirated, just it showing up there like it was might raise red flags is what I'm getting at.
I did a test run, and the crash you described is actually caused by the rewrite code trying to read SVI files of the master branch by the way. I need to make some changes to how some of this stuff works. Writing that save meta reader and reading the values from some of this stuff is getting interesting to say the least. Most account saves should be fine, but other types... That's where it starts getting interesting.