[dotnet00]

ISP isn't everything, even in space, as you don't have infinite time to get places, transfer burns etc are more efficient when closer to being instantaneous (in terms of dV) and capture burns need to happen within a fixed timeframe.

Also I think what they meant is that the engine's thrust dictates the height above it that it can lift. So lots of larger low thrust engines = short and stubby rocket, which adds all sorts of limitations (construction, transportation, aerodynamics).