I agree that Mania's scoring system is pretty solid. And to answer your question, I think it would help to look at the math behind the scoring for Mania. Here is how it works.
Score = BaseScore + BonusScore
BaseScore = (MaxScore * ModMultiplier * 0.5 / TotalNotes) * (HitValue / 320)
"BonusScore = (MaxScore * ModMultiplier * 0.5 / TotalNotes) * (HitBonusValue * Sqrt(Bonus) / 320)
Bonus = Bonus before this hit + HitBonus - HitPunishment / ModDivider
Bonus is limited to [0, 100], initially 100.
MaxScore = 1 000 000
ModMultiplier = The score multiplier of the selected mods (difficulty reduction and/or nK)
ModDivider = The punishment divider of the selected mods (difficulty increase)
Judgement HitValue HitBonusValue HitBonus HitPunishment
MAX 320 32 2
300 300 32 1
200 200 16 8
100 100 8 24
50 50 4 44
Miss 0 0 ∞"
-Pulled from the scoring wiki
The biggest thing to take into account here is the bonus score. I.E BonusScore = (MaxScore * ModMultiplier * 0.5 / TotalNotes) * (HitBonusValue * Sqrt(Bonus) / 320)
Bonus = Bonus before this hit + HitBonus - HitPunishment / ModDivider
Bonus is limited to [0, 100], initially 100.
Since misses and 50's make you take a big hit to your bonus score. My guess is that you hit these 50's and misses (and some
times 200's and 100's) to keep your average Bonus Score lower than the other score where you had less 300's and rainbow 300's. It is sometimes deceiving, but hitting these 50's and misses at the right time can be detrimental to your bonus score... lowering your max potential score by a good amount.
In more simple terms, hitting three misses in a row is not nearly as bad as hitting three misses within 50 notes of each other, the latter has a worse effect on your average bonus score.