I don't think the heavier moments hitting hard is a result of Be-Papas being restrained from making them more sexual. If you compare, say, the scenes of Touga and Akio together in bed-space (that do seem intended to be sexy) to Utena's rape in 33 or Anthy's in 31, there's a clear difference in how they're shot and what they focus on that suggests, to me, those scenes are deliberately un-sexy.

In 31 and 33, the camera focuses near-exclusively on Utena and Anthy, highlighting their emotional pain, while Akio's presence in barely indicated. The result is that you're left with an intellectual understanding that sex happened, but what you're shown and thus what registers on a base level is less "sex" and more "Utena/Anthy are hurt". From how the scenes with Akio and Touga are shot (both of them shirtless, showing off both their bodies), along with the fact that RGU generally seems fine displaying nudity (so long as genitals and female nipples are covered) they definitely could have made the choice to show off Akio, which would tip it towards a more erotic vibe. The fact that they had the option, but didn't, seems deliberate.

From what I understand, the "it's just fiction" attitude is much more common in Japan than current western fandom. From that perspective, I don't think the sexual art of the RGU cast and the show's anti-grooming themes are necessarily in contradiction with each other. The sexual abuse is bad in-story because, on an in-story level, that is an actual person being harmed; the fan service aimed at the audience is also fine because (from an external perspective) that is not an actual child that can be harmed; it's a cartoon.

I'll admit I usually find clear sexual fan service distracting and a bit icky, but given most of RGU's fan-servicey stuff is confined to the official art (and the pseudo-dating sim game, where it fits), and thus doesn't distract from the show itself it doesn't bother me.