Why was the Starfleet Corps of Engineers team in the book series by that name given such a small ship to use? A Sabre class IIRC, one of the smallest regular ships in Starfleet. IIRC, Duffy the former second officer was designing a ship that he thought would be better for the SCE based on the Norway design. Will the SCE ever get a ship more customized to their mission needs?
Why not? As you say, it was a team, a relatively small team of specialist/troubleshooters. It wouldn't have made sense to use a huge ship to ferry a couple of dozen people around.
Some of the modifications Duffy was thinking of were incorporated into the ship when it was rebuilt after Wildfire. In any case, they were given a small ship for two reasons, one in the box, one out of it: The ship's missions are ones that are easily handled by a small, mobile team, and I wanted a ship with only 42 people on it. The reason for the latter is simple: every Star Trek series has crews in the hundreds (a thousand on TNG), yet the same seven people seem to be doing all the work. Part of that is the nature of storytelling, but I thought for SCE it made more sense to have a small ship where we could actually get to know the vast majority of the crew.
As the book "Wildfire" makes clear, often the team is involved in salvage, recovery, or investigative operations that require large amounts of open space. Duffy himself makes those points and regarding the inadequacy of the current ship in that regard.