I've spent the past few days poking around in Sauerbraten and I'm very impressed. I think the active area of my game world will wind up as a Cube 2 map.
I also am concerned about scale, but not overly so. I haven't dug far into their forums yet but I too had originally thought that 2.5 feet per default grid square was about right; now I'm not so sure. If the default player model "Mr. Fixit" is assumed to be average height, say 5' 10", then the default grid is more like 3 feet. From what you're saying, Jason, it sounds like it's up to the mapper to decide.
A bigger concern for me is that I have yet to figure out how to keep up with where I am. If I'm doing a few square miles of outdoor map, and I've figured how to convert my own hex map coordinates to their square grid, how do I find a particular location on the grid? I'll figure out something. Every day I play with it a while and figure out something else.
I think it will help my players' immersion to actually walk down the roads their characters have traveled and recognize the locations they've visited. I think I'll enjoy that myself.