Pulled out a rough mock-up of what the end nacelles might look like when "transforming" between flat and sphere ends. The "raised panel" would be the middle section of the flat end extending/retracting. The grill pattern would be panels that could slide in (slightly) and change color/recede into shadow.
Although some good work has gone into these, I think it is unnecessary to to explain oddities such as these as they were not intended. The only reason we see such things is purely because of budgetary reasons. TOS:R made no such attempts to explain these so why should we? The different nacelle endcaps we see are from two different models in three different configurations.
The caps with the clips on them are from a 3 foot study model build for The Cage: this model was not intended to be filmed but because of monetary and time saving reasons it was used in the first pilot. It is interesting to note here that the large 11 foot model was only used in ONE shot during this episode; the opening establishing shot, and at this time the end caps on that model were completely smooth with no clip detail at all, again due to time and money constraints.
I don't see any need for an in-universe explanation.
The endcaps with the holes in them are from Where No Man Has Gone Before and the reason we see these in the series are, again, for budgetary reasons... Footage of the 11 foot model taken during the filming of WNMHGB in 1965 was taken and used as stock footage for the three seasons of the show form '66-'69 to save money on filming more of the same shots, nothing more. At the time such small differences were supposed to go un-noticed. Who would have guessed that years later now, fans of the show would be picking at every detail.
It's a lot of fun as we all know, but trying to explain things like this makes the Trek universe less credible and more un-believeable IMHO.
Again, some truely awesome work here!
BTW, I noticed that the forced perspective engineering set has been taken a little literally; it's not supposed to actually be distorted to a point like that.
In fact I was sure that those pipes go directly up through the warp engine pylons to feed the nacelles directly! This idea would also support an engine roon in the engineering hull