I guess I was wrong. I assumed (incorrectly) that the AVWizard would adjust the ModeLine. Adjusting just the UI would prove more compatible and be much easier to program, so I understand why it was done that way. However, since LinuxMCE is moving more to the Desktop arena it should be changed, which is what the mantis bug is about no doubt... I'll have to actually read it now
In order to do this you'll have to first, back up your xorg.conf, re-run the AVWizard and select any resolution that works (it's unimportant which one) and be sure when it ask about the zoom stuff do not change anything (just leave it zoomed in). Now go to the admin page and change the MD and Onscreen Orbiter devices to the 1080i resolution, reload router, regen the Orbiter and adjust the xorg.conf to your 1080i resolution from the xorg.conf that you backed up, and reboot. Now you can tweak the Modeline using the guide in my previous post (again, I do not envy this process). Once you got that set back up that modeline! Then change the MD and Onscreen Orbiter devices to the true resolution you selected after all the modeline tweaking (only if it really changed and keep the tv standard setting), reload, regen, then edit your Xorg.conf to use that Modeline and reboot.