The only reason why absolute coords would matter is if you configured your screens to use something like xinerama or twinview instead of making them separate screens.
I may be a little fuzzy on the X terminology for things, (trying to remember the multi-zone setup I did for a company a summer ago) but I recall finding the making them separate screen sessions was the easiest setup and didn't require the apps to do anything special. XI2/MPX wasn't available at the time so I had major issues with simultaneous dragging making X explode.

