I'd always believed that the Sovereign class that became the Ent-E was nearing completion when the Ent-D bought it and Starfleet re/named it to continue the tradition. In regards to the refit the Ent-D had received prior to Generations, I assumed it was due to the seriousness of the Dominion threat after the Odyssey was so easily destroyed.
"Men, we're facing a grave threat. The Odyssey was destroyed. Take the Enterprise and turn down the lights. That way no one will think we're home."
"But, sir. Should we take the hide the shield frequency...or at least not display on monitors?"
"No...but better add a couple of extra stations to the bridge just in case."