We know 話 can be used as a counter for, including but not limited to, anime franchise episodes. But if I understand it right, 話 refers to an episode as a completed, ready-for-consumption work.
That doesn't seem to be the exact same case with 本 though, which, apparently, can be also used for similar purpose. In this interview they refer to episodes with 本 (random quotes):
But they also use 話 when they refer not specifically to a number of episodes that Nakamura's got to work on, but to an episode itself which is a part of a completed franchise:
At the same time, we know that 本 is usually used in regards to movies, computer software, and video games. And here someone suggested an interesting theory as to why. If we were to base off of that theory, any episode is a collection of cuts, which in turn are compilations of cels with drawings (not really true these days, but whatever), and any episode also consists of lots of writing (including writing that precedes the drawings itself and sets the way they are going to be, essentially being the ソース), hence 本.
So my question is – am I right assuming that 本 is the counter that should be used specifically in the context of an episode production, but not when it's finished? If so, how come it is that way, providing the theory above is wrong.