Just thinking out loud here but if I was going to take this approach I think I would make the first box of each run a two gang junction box with a partition barrier. Something like this: http://www.smarthome.com/25402/Two-G...-Inches/p.aspx
I would use two GFI outlets in the one box and then run my load outlets off of this keeping everything GFI.
You could then divide the two 110’s inside the box and keep it all separate for someone coming along in the future.
I don’t know if that is to code or better than the OP’s setup that I gather is to code also. I’m sure the pros will sound in on what code says.