Adding author intent to the mix seems unnecessary to me, when there's already so much material that "actually" describes the fictional universe, in the "with our own eyes and ears" sense.
...the two times this occurs in "The Alternative Factor" there are gaps in the "stealing event" where we cannot say either way if the ship exhibited a "brown out" event like we see in other episodes.
Agreed. But our heroes would probably mention past brown-outs or express other concern about the observed effects of the thefts - whereas the dialogue merely has them claim that the ship cannot operate at full power without "the crystals", but never indicating that such a limitation would actually have kicked in.
Which might mean that losing ALL the crystals is bad, but losing just 2+2 isn't...
In any case, the articulation frame in "Elaan of Troyius" appears to only hold one paddle of dilithium, and sabotage to this one cripples the ship - yet in "Mudd's Women" three crystals were lost in sequence, without
Scotty running down to Main Engineering to replace a burnt one with a fresh paddle each time. This might favor an interpretation where something fundamental changed about the engineering arrangements, and a move from a four-slot device in "Alternative Factor" to a single-slot frame in "Elaan of Troyius" would fit the bill.
On the other hand, I've always seen the articulation frame thing as a waldo of sorts, a tube-mail system for accessing a deeply buried reactor's dilithium innards. The system might well handle more than one frame, despite only one popping out at a time. And given how rare dilithium seems to be in that era, the ship might have varying numbers of paddles in its reactor at different times, there being another acute shortage during "Elaan"...