...And why would an arboretum have windows opening into space? Much less ones that glowed an intense blue light? The arboretums we saw had a pleasant yellowish glow inside, and the plants within did not seem to be suffering from erratic exposure to starlight.
Whenever the warp power was severely taxed or drained, it would take time to build them back up again, or "regenerate" them.
But none of those references indicate that fuel would be replenished or that finite resources would not
be drained. A gasoline engine would need to recover from damage or cold, too...
The two examples of great endurance are dubious, too. "Mark of Gideon" does not deal with propulsion, but with the survival of two people in a situation where the rest of the universe for all practical purposes has ceased to be inhabited. And "By Any Other Name" deals with alien modifications to the drive, these consisting of the addition of a thingamabob into the loop - quite probably a power source of great endurance, as the one performance spec of the ship we see increased beyond previously established ones is endurance at speed.
As far as I know, the TOS movies were inline with what was depicted in TOS. What specific examples were you thinking of?
The visual and verbal references to antimatter intermix at Main Engineering in TMP, mainly. The full Probert or Puttkamer ideas weren't explicit yet, but the focus was moving away from the nacelles already.