I was glad to see Witwer address it, not because there had been any huge controversy, there hadn't been any. I've personally never seen RDM say a word about Witwer and whereas he did mention something that might have been related to Witwer, it wasn't anything negative. Just one of those generic "the character wasn't working" or something like that. It was vaguer than that though, more like "there was a character in season one that wasn't working, but we sorted that out" which might have been about Crashdown or might have been about a million other things.
I think what Witwer refers to in that clip is that comment though. It's just a nice opportunity for him to offer clarity.
For whatever it is worth, I don't think RDM would ever say something that he thought might hurt someone's career. So a comment like "the character wasn't clicking" can be taken at face value, rather than being code for something alarming in a professional sense. That's just based on how careful he always was in the podcast and in interviews. Of course, there is fan math :-) Like the time they did a round-table podcast and while being extremely careful not to name the director, the cast and Ron Moore were full of "We hated that guy! Every last one of us! There was almost a rebellion on set!" stories (the cast brought it up, RDM didn't deny it, but clearly held the reins on the "we're not naming names here" thing). They were honest about their personal experiences without impugning anyone's character. It took people listening to the podcast four minutes of ye olde Google-fu to figure out "Yup, they're talking about Felix Acala. Interesting, he works like crazy."
But they always were careful not to slam anyone. Unfortunately, Witwer exited around about the time Paul Cambell (Billy) did and Paul Campbell is prone to being goofy, it seems. Nothing dire, but at the time he had a blog, it didn't reflect a high level of diplomacy in terms of professionalism -- here's an example, his IMDb biography
shows that pretty clearly. It's not that he's unprofessional, it's that he's upfront about not being a science-fiction fan and that he didn't actually want to commit to BSG because it was scifi. He also likes to be sort of silly (me too, so I'm not judging). I think when talking about the mini on his blog, Campbell said something like he was pleased to see it wasn't "a complete steaming, pile of crap". Funny, but also kind of wince-inducing.
Anyway, Ron Moore was always very nice about "hey, the actor (Campbell) didn't want to commit, it wasn't a problem but we did eventually have to write him out because it made planning stories more difficult" no rancor, or ill will. However, if you're Witwer and the same guy only ever indirectly addresses your departure from the show, I can see how it might cause a case of "For the record...I'd like to say...".
Long way of saying, I liked how Witwer and Moore (if he was actually talking about Witwer in the "character wasn't clicking" or whatever equally mild language of "nothing personal" was used) basically end up saying the exact same thing. Witwer just sort of slid the fact that most of what he did ended up on the cutting room floor in there, while praising the show. While Moore's "wasn't working" also encompasses "Yeah, for whatever reason, his was the stuff that always ended up on the cutting room floor...it just wasn't working." (as in "the material" and not "the actor").
Also, I think the whole thing where, as far as I know, Ron Moore never actually directly addressed anything having to do with the actor, can end up being read in the opposite manner. Moore's pretty up-front, while still making sure not to slam anyone, so I've always sort of taken the "he never really said anything" to mean: I don't think he actually remembers much about Witwer. He was focused on running an entire show, juggling a bunch of characters and there wasn't anything personal.
It's also clear that Witwer knows that, because he also tosses off the seemingly sincere "I don't know if Ron Moore even remembers this..." without being nasty about it. On a production of any size, or really in any work environment, you just remember the things that were problems or drew a lot of focus. Like how RDM was asked about Campbell's departure, partially because the actor was out there giving interviews, talking about not liking science-fiction. I mean, that's a freaking problem if you're the show-runner of the science-ficiton show he's on.