Arseholes can be nice and nice guys can be arseholes, congratulations, you have identified a different problem from the one being discussed. The real issue is that the LI's who favour the Chick version of the MC will hear about his Dik choices. The fact that he is a Chick in his heart and mind is of no consequence since they aren't psychic; they are forced to judge him by his actions and they're right to do so.
But many of the major choice actions are not ones they would ever know about, so how does that colour their perception of him? They can only truly judge him by how he has been with them and if he's been caring, attentive, and just an all around good guy then they would like and accept him if that's what they're looking for, but if he's been cocky, obnoxious, and inattentive, then that would put him in a bad light and make him more likely to be rejected.
Therefore, the minor choices are more impactful to how these character perceive the MC than the major choices.
The Dik/Chick bar represent the MC's actions, the Dik/Chick points represent his thoughts. Only the player of the game can know what the MC's thoughts are, the NPC's are forced to judge him by his actions.
You are free to have an MC with severe cognitive dissonance, just don't expect the NPCs to recognise and forgive it.
The points do not represent the MC's thoughts as they are pretty much all tied to actions. A few of these in the first episode were tied to the MC's thoughts and maybe this was how DPC originally intended it, but as the game has gone one they are more tied to his actions, like sniffing Maya's hair, spying on Bella, and sticking his finger in Lily's ass.
Doing these creepy, obnoxious, and often juvenile things are the actions that the NPCs can truly judge him on because there are more of them and build a better picture of the MC than him having a couple of fights, not being nice to a guy who was an asshole to him, and smoking a bit of pot.
The status points are a far better metric by which to judge the MC than the affinity, but even so, characters who judge the MC because of a status determined by actions that they couldn't possibly have any knowledge of is ridiculous. If anything, individual RP with each character or group of characters should hold the greatest weight of all in determining how he is viewed by them.