I use the single sheath for my Vic swisstool, so I can easily swap it from belt to bag and back. I don't find the keeper straps rub much, it does happen if the sheath gets to an odd spot though.
I also have a flashlight sheath, I think mine is the 5inch. I just tried it, and my swisstool does fit. it seems like it might want to turn 90* to the belt (if that makes sense) But I don't think it would be much of a problem. My SOG powerlock also fits, a bit tighter. The only thing is, the tool is fully enclosed in the sheath, so it takes some fiddling to get out (squeezing the bottom seemed to push it up reasonably well though) the 4inch should solve that problem a bit for you. But there would be no room for the tool kit.
I think the flashlight sheath has a better belt carry, but the molle sucks. So if you primarily belt carry, and don't feel like removing it (or don't mind undoing your belt) then I think the flashlight sheath would work better. Testing in-store would be the best though.