This is all my interpretation, but I think this is supposed to be a commentary on how manipulative and contrived most yaoi stories are.
Think about it, how many yaoi stories have you read that go something like this: uke meets seme and at first the seme comes of as a jerk (in some cases they even do something questionable to the uke, or even go as far as rape). So the uke spends the majority of the storie hating the seme, until at some point, he sees himself in a dangerous situation, where he is saved by the seme. From then on, the uke realizes that the seme is a good person, and they become a couple. Happily ever after, etc, etc. (Hana no mizo shiru comes to mind but there are a lot others).
In those type of stories the "dangerous situation" the uke sees himself in is basically a really easy and convinient way for the author to make the uke change his mind about the seme, and give the readers the happy ending. In Color Recipe, we see how this trope is subverted, because in the end, we learn that the seme was planning everything, putting every little detail into place and manipulating the uke's emotions, the same way the author normally manipulates the readers emotions via convinient plot elements, instead of having the character's emotional progression occur naturaly and realistically.
This is also comment on the fujoshi community as whole. We have become so used to the whole "true love starts with rape" thing that we don't question the trustability of a character that sexually harassed the uke in the first chapter. In any normal story we would automatically question the intentions of the seme when he starts to be more kind towards the uke, and we would probably be very upset that the uke hasn't put a restriction order on that guy yet. Because it's been so normalized in yaoi, we all fell for the seme's act.
God please end this flashback