I just assumed they were reusing stock footage. Probably helped along by the fact that I'd already gone through "The Making of Star Trek" and "The World of Star Trek" before TOS hit a regular syndication time slot of weekdays at 4pm in Denver (before that, it was hit or miss on any random Saturday). So I already knew about many of the weirdness of production, including the whole matter of there being two pilots that bore little resemblance to the regular episodes.
But then, I was always an overly observant and analytical kid. Never believed in Santa Claus, either.