The reason for not going all the way to the floor goes like this...

In normal use, the MC piston never goes all the way down. The last part of the cylinder might have crud, corrosion, or maybe it's just not polished smooth like the part that gets used all the time. When you pump all the way down, you work the piston seals against that rough(?) part of the cylinder and maybe damage the seals.

When you're bleeding the clutch, that doesn't make sense. The clutch MC goes all the way down every time you use it.

This makes complete sense to me, but like I said, I've pumped brakes all the way down MANY times without a problem. Maybe that's just because I never let my brake fluid get real old...