My BMC has only 3" clearance under the bike.... I have to stop and get my weight off the bike to go over every speed bump
As for the forward controls... I have had my foot pulled off the peg in a corner and that can throw your balance off as well as twist the knee. Now when I ride I feel the road with my foot in the corners but it took a quite few miles to get used to this., The corners of my boots heels are work off too. .
So I guess go as low as you can for the look you want, ride and get used to the way it feels, ride safe and have fun.
PS:: I think 3" clearance is a bit too low, but I just havent gotten around to adjusting the progressive shocks to bring it up. that would makes it a stiffer ride too.