So, the current version is mainly the main/harem route but there are some scenes and kinks which shouldn't be expected, based upon Uberpie's speaking, to remain in that route once the two separate versions of the game are released (main/harem and netorare). He has mentioned that he doesn't expect the crossdressing scene of the MC expressing as Winifred, in particular, to continue in the main/harem route. Pennyworth, the fourth personality of the MC (Blue, Red, Winifred being the other three) probably won't exist in the main/harem route.
Danny is not a sissified character. Danny is a femboy (in avoidable scenes). Yes, there is a difference. I haven't seen anything about how that plotline will be affected by this splitting of the game into two (and then, maybe, three with the friendship/sharing) routes. And since Danny already has a sizable following, regardless of other proclivities regarding harem and netorare, I would assume Danny will remain in both versions of the game.
Particularly since Danny's storyline is already coded as such to be (nearly?) completely avoidable as it is, I don't necessarily see Danny's optional scenes removed from the main/harem route, but adding other characters with sissification, etc? That might be a bit much for a vocal individuals in the fandom. Which goes to the question why are we getting two completely different versions - netorare and harem - because there has been enough whining and wailing from a number of anti-netorare people (not all) that they can't stand even the option of netorare in their experience of playing. Some of this is due to coding issues in a previous version which didn't hide an option to a preview of what might be seen in a netorare version (Mary and Darnell in the gym).
I would assume the same - as would the vast majority of people - that netori is not considered NTR, should not be considered NTR, and using the same three letter acronym for various definitions within the same field/believe system/sexuality/etc whatever is highly problematic and should be discouraged rather than continued. Acronyms are supposed to shorten and delineate. Thank you for your part in using the terms, rather than just relying on the three-letters.
The NTR/netorare route is a completely different storyline/route/quest line than the friendship/sharing route - at least it has been presented as being planned as a third route after the first two, main/harem and NTR, routes for at least 3 years.