@theSLAYER, looking at a previous save I had those flags were set even before I scanned the Magearna QR code. So I am not sure if those are the exact flags.
But, thanks to having a previous save, I was able to get the constants that were changed between me not scanning the code and after me scanning it. The only thing to note is that I hadn't done QR scan before the Magearna so there may be some other flags mixed in. I am going to try to figure it out myself, but here is the Flag Diff for anyone who capable of properly doing event constants research:
IsSet:
Unset: 4681, 4682, 4688, 4713
Event Constants Diff:
55: 0->75
194: 30->0