So let’s talk about the real reason why the Tomokofag is upset about the cross-character bits in synergies - simply, the answer is it interferes with his self-insert fantasy.
The fact of the matter is that Wonder is - by necessity - extremely bland as a character. That is how he functions as a self insert. And in events the self-insert acts as a sounding board to the actual character, who talks out their issues largely by themselves.
However, when you have these crossover synergy events, you have interactions between 2 real characters, and they talk to each other - bonding, empathizing, etc. this is chemistry.
And while this is happening, it becomes even more apparent that Wonder (i.e. the self-insert, i.e. the player, i.e. tomokofag) is a third wheel, and doesn’t really do anything with the real characters and is largely irrelevant. And sure the game will say something like “wow, you being here helped me make that decision (that I was already going to make and all your text options just affirmed)” but that’s hollow platitudes and it’s easy to recognize that.
What you end up with, is that the relationship between those two characters is a lot more functional than anything going on with Wonder, and so the Self-insertion is broken. If this wasn’t a gacha and we had more than 10 male characters (and they let the male and female characters interact - a big no-no for the self-insert crowd), ships between synergy shared characters would be inevitable (which destroys the self-inserter), but since it’s all girls (or in Kayo’s case, a family member) that’s mostly avoided. However - especially with Merope where her Narumi fixation is very prominent - the game has essentially set up Yuri ships in fear of creating straight ones, much in the same way many other series have such as Love Live.
And that’s really the end point of it, because Tomokofag is raging against the thought of being NTR-ed by Kotone, which the writing has inadvertently done to him.