Ive been doing tests and it never seems that much. Usually like 11k after beating the level 4 boss and beating Darc Seed.
For the fuck of it I put on a game genie code that prevented me from dying. I just went HAM on everything I could, flying thru lasers, destroying every little piece of stuff I could to get points (except from one area that prevented me on hard but you can do it on easy. In level 4, that area with the 3 purple balls where the ground shoots bullets at you, you can actually get under there. There are shootable rocks under it. The points that I missed would have probably added up to 2000 away, maybe 3k.
After beating the level 4 snake boss, I got 489500 and after beating Darc Seed, the games final boss, 504,200. Which is a 14,700 difference. Even with the ability to not die, I still have no idea how bert got that score haha.
BTW if anyone wants to do some research, try this GG code: AVXTEISZ