By that logic aren't grinding affection points and blindly looking for events also important parts of the game?
Yep. Grinding is also part of the game. But... it's too boring

One "importan grinding part" that I can remember is when Rin disappears in Chapter 1, and the points needed for her can only be collected by talking to Haruka.
Unfortunately, this part is completely missed during autoplay. Had to sacrifice it.
From this, I take that "Schadenfreude" is put on hold, as it becomes available way before the first beach trip, and seeing it before it will trigger bad homie route, which isn't green path. A similar issue, but less troublesome, happens with "Matador", as seeing Chika's onsen trip before "Abyss" will trigger the Yumi rejects blackmail route (which also isn't green route).
Yes, "Schadenfreude" not available until the trip with Chika to the onsen. And "Matador" until "Abyss"
Also, Kirin's "Four hand massage" and there was something else.
No missed events were detected during autoskip testing.
But you can disable the mod in any time. So if you made a wrong decision yourself, the mod won't fix it then you enable it back.
Also, you decide whether to fuck the mothers or not. Mod hints it not good decision, but it allows you to make such a choice. Accordingly, some their events will be skipped further.