The rapier evolved from the old cut-and-thrust swords, so yes, armour penetration was it's priority. I understand rapier-like straight swords were in use by some cavalries during the late 18th and early 19th century alongside sabres, but against pike formations? Very curious, I'd like to know your source for that so I can read in to it 
As for working best with a dagger, well, that depends on your swordsmanship school. Italian schools of historical fencing are fond of rapier and dagger, if I recall correctly.

As for working best with a dagger, well, that depends on your swordsmanship school. Italian schools of historical fencing are fond of rapier and dagger, if I recall correctly.