I dont have a problem if you make an NTR game, I only have an issue with optional NTR in games that arent about NTR.
Like you have a harem game about you fucking girls and having a harem but then you add NTR which is what bothers me because the NTR is in total dissonance with the rest of the game as it doesnt contributes to the harem theme.
Being optional doesnt works because:
1- The game is spending resources in content I dont care for which is troublesome as its resources it could have been spend on more content that I care for.
2- You cant finish the game 100%. You have to get cucked to fully complete the game.
3- It fucks the characters and narrative. If you make a badass MC and he gets cucked then the character is no longer a badass as wether you like it or not people will associate the cuck as part of his characters (Like Rowan will be a cuck no matter how much the Dev adds scene of Rowan being a badass, the cuck stigma will never wear off).
The females too. Now the loyal and pure waifu is now seen as an slut who will dump you for the nearest dick and now the pure path is no longer pure. Users will no longer buy her as someone they want to romance or pursue (See Alexa).
4- The patreon model works against it because now you have to split resourcess to appeal to both so unless your artist (Or you if you render) is a workhorse you are delivering gimped content for both sides, jack of all trades Master of none. The other option would be one update for NTR and another for non- NTR which makes the wait more ardous.
5- It can stunt your growth. Seeds of Chaos prides itself as a multifetish game and has been a long time in the race but it has had the slowest growth out of its peers despite the work ethic and art being beyond and above said peers. But really the game being known as half NTR and half Rowan made it so it had such an slow growth. Taffy Tales also sports the same idea but the dev realized his growth was being stunted thanks NTR so it focused on the MC having sex content and now it has grown a lot (Though NTR will be added soon so we will see how the game fares after NTR content starts to shime in).
But in the end its your project and motivation is essential so you dont burn out so if you want to add NTR go for it but if you want money I think not adding NTR is a safee bet.
I disagree in quite a few parts that you have said:
-You are right in that a harem game that presents itself as just that doesn't need to add NTR even if it's optional, unless it was planned from the start and it was kind of "fight to make your harem".
-It doesn't fuck narrative or characters, what can fuck it is if they are really easy, I can believe Alexa having sex with Andras when she fears for Rowan's safety, in fact if we wanted the narrative to be adecuate then Alexa would have sex with Andras as a story event because the option to sneak around and risk everything isn't appropiate or even sensible at all in that situation.
-Real relationships have real problems and Alexa getting mad at Rowan's cheating for example is normal that it could push her towards cheating herself, she doesn't feel like a propety or part of Rowan's harem but as his wife!, this is very different.
Overall on seeds of chaos the NTR aspect adds to the narrative and characters, another thing is that you dislike the content itself.
In fact seeds of chaos would be more true to it's narrative if many scenes (I'm not talking about the NTR ones but many different ones) were NOT optional. I don't like gay stuff but I do believe Andras would have forced Rowan to have sex quite a few times, in fact at the start I believe both of your "rulers" would have forced you to have sex. Other characters like the librarian I do believe they wouldn't care about your opinnion of if you prefer to give her your semen this way or that way, she would just do it in the way she wants and be done with it.
But well, the game can't make that because some people wouldn't accept it, even if you can skip the scene and don't see what you dislike of story events they would be like "but I know it happened!" and this useless comment is what doesn't let most of the games to have a more complex storyline related to sex. You know, in many games that I have played from japanese many bad things happen as story events, one of the most liked ones is Sengoku Rance and in that one Kouhime gets raped "
in the true route", in fact the game that saved Alicesoft from bankrupcy was a game called Kichikuou Rance and this game is the king of bad endings for characters, while most of them can be prevented if you act fast enough it is more than possible that in your first playthrough you will encounter really sad things (like the death of Sill for example).
Lastly... no, that the game gives a possibility of the girlfriend's cheating doesn't make the MC a cuck unless we are under that possibility, not all games are made for you to obtain 100% in cg's or content, the same as Undertale gives you the option to just leave it on the happy ending or try to get the genocide run.