Man, in game terms they are just a season and actually the MC had sex with both, only in a case he is are not 100% sure it actually happened (he is however certain to have licked Mr.L in the under the desk scene) in the other case SHE was hallucinated when it happened.
Note that the MC has not actually had a real full intercourse neither with:
A. Kate.
B. Lindsey
Still the scenes involving them are actually in the first case the most extreme and perverts in the game, in the second the most romantics, wholesome, selfless ones you could imagine.
So, this game allow you to be in the same time a literal Motherfucker (Jo), a Rapist (Stepping on the Rose is THIS, no sugar coating, please) and in alternative having a regular relation, an incestuous one (with Flora), a classical mentor/disciple sex relation and in the end one with Lindsey in which the idea sex is even secondary to a profound soul-bonding.
So, you could actually choose (actually not, you still could get it all at the same time) between satisfying your most basest instinct up to commit crimes and at the contrary elevate yourself even above the sexual urges themselves.