My take on the situation:
The E-D was configured out of the yard as an long-term exploration ship, for deep-deep-space missions. Because of this she had to carry consumables like torpedoes onboard. Yes they could replicate more, but that's energy intensive.
The deep-deep-space mission never happened (Farpoint) so she was recalled and some of her "excess" inventory offloaded as now she could zip to a Starbase for resupply.
The E-E on the other hand was configured out of the yard for combat because Starfleet was on a war-footing. From the Dominion War to Borg Incursion to Sona Nonsense to the Romulan Unpleasantness the E-E has had little time to Boldly Go... every time she Boldly Goes she runs into a combat situation, and has to return to the yard for another refit. No wonder the profiles don't match anymore.
Now assuming that Starfleet eventually gets back to Boldly Going and exploring the Sovvies will either be mothballed or refit for scientific and deep-space exploration. That includes removing some torpedo bays, adujusting inventorys and internal layouts. More labs, diplomatic rooms, possible civilian quarters...
Comparing the Galaxy as seen in TNG and the Sovvie as seen in the movies is pointless unless you factor in the political enviroment and mission profile, as I did above.