I don't think it's a glitch or a bug. You don't get to see the middle/right route ending if you lose too many fights and retry too many times, which is exactly 10 times. It's always 10, not some other random numbers. So my guess is that it was intended.

We always have to refer to the rule, and I don't see that run breaking any: He finished the game with Flandre. The run starts from stage one(we can clearly see "第一話")

You could change the rule, but since he already submitted the run, I say you shouldn't. In my perspective, that'd be unfair. Consider creating another category with "no major skip" or something like that instead.

But it's always up to the moderator. I understand how hard is it to manage the leaderboard, so I wouldn't complain about decisions you make.