Most difficulty mods increase the score multiplier. Sudden Death and PerFect are the exceptions. Why would these, which can make a beatmap more difficult, not affect the score?
Answering from the perspective as a player, since the developers might have a completely different reason, as stated from SaintWacko's comment.
SD/PF are just there to force a player to full combo or get a perfect accuracy on a map, respectfully. The difficulty gained from those mods is subjective, not objective (unlike HR, DT, HD, or FL).
Some example I can think of:
What would be a better score?
- A 100% 4 mod (HRDTHDFL combined), or
- the same score but with PF (HRDTHDFLPF combined)?
Both players did the exact same score and why would one be worth more points?
Well, one might argue that the PF score is more impressive, but still, it's the same score.
My personal perspective on this one is that those mods are just used to make a statement, or just to "flex", really.