A quick and dirty explanation for the Enterprise E's altered appearance: Maybe she took part in a fleet-battle at some point and being THE ship of ships she suffered some serious damage which had to be delt with, so she was torn down and refit to Sovvie Block II standards.
The damage incurred in FC required a lengthy yard stay. Here she was altered to Sovvie Block I-A standards.
How long between FC and Insuckrection??
After the battles in Insuckrection the ship is subjected to another lengthy yard overhaul, while in the yard she is refitted to Sovvie Block II standards and given a serious upgrade in firepower.
Post refit she sees combat duty mopping up twords the end of the Dominion War and its aftermath. After a year or two of near constent combat and "firepower diplomacy" she enters the yard AGAIN for a refit, and this is the configuration we see in Nem.
The Sovvie is a hanger-queen design in my RPG universe, it was built rapidly using bleeding edge methods and materials and fitted with a mixture of old and new technology... it was intended to get a battle-capable ship to the front lines ahead of the "next Borg incrusion" but the few that were built proved to be tricky at best, with the Enterprise requiring over a year of shakedown and return trips to the yard to iron out some of the more serious flaws. The original Sovvie and the two other non-canon ships were the same way.
During combat operations they proved difficult to repair in the field due to the mismatched generations of technology (some key systems were built from scratch and there were no spare parts in the field) and exotic hull materials made welding/bonding difficult without special equipment.
Lastly, due to thier intended role as front-line units they routinly got the crap kicked out of them, often vigorously... leading to the problems mentioned above being maginifed several dozen times.