I never saw those, but might be interesting (and conducive to the interests of this thread) if they were flaccid, at least most of the time. I've seen fan-made nude edits before, but usually they're huge and often messy erections that don't even fit the context or mood of the scene.
One of the things that makes permanudity so attractive is if it does not seem like the characters are actively trying to be porn for some audience to watch. It helps if, despite not wearing clothes, they don't seem "exposed," if that makes sense, because what they're (not) wearing just isn't relevant to them and they have not been culturally groomed to be ashamed or self-conscious of their own bodies. Instead, they're just being their honest candid everyday selves, up to and including sex, but in any event are not trying to prove anything to anyone else. They seem authentically comfortable and confident in their own skin.
Art by Cooner. In the case of this version of Bebop and Rocksteady, it's not necessarily that they never had body shame in the past, but have chosen to completely banish it from their lives. And when it seems clear that it's simply not relevant to them, then they no longer even seem exposed. Honestly, it's rather strange that these turtles care that B&R are naked, considering they're not wearing clothes either, so it's really not that different except maybe that B&R's junk is visible and the turtles' isn't.