Almost every device I've seen with "chapter skip" functions do not use the channel buttons

That's true with most devices in the past, but now with more digital convergence devices it's not going to be true in the future. For example on Tivo/ReplayTV it's really useful to use the chapter skip buttons for instant replay & jump to live. The channel buttons are still needed for changing channels. The need for both is also going to be evident on DVD video recorders when they arrive.
Even on my old Sony SLV-700 VCR I like to use the chapter skip for fast scan forward/backward, which behave differently from FF/REW which have to be held down.

It just seems to me that there is room on the remote to stick in a couple more buttons in between the volume and channel buttons, especially such frequently used buttons as "menu" and "info" which deserve their own button. The LCD area is fine for "rec" I guess, but it's an awkward hand move so I only want to put rarely used buttons up there.

I still can't believe the MX1000 has a 5-way joystick but no "menu" key, forcing you to give up "pre channel". Not to mention no pause key or chapter skip. I wish they would submit mockups of their designs to the power remote users here on remotecentral before going into production; we could point out the obvious flaws like that.