My guild uses Zero-sum DKP, so we draw from the same DKP pool regardless of the event and who all is there. For signups, I don't know if this will help you at all, but we just schedule two seprate events and let people signup for whichever event they would like to do. So far it's been ok like that.
Attendance is the only thing I can't find a work around for.
I think it would be easy to compensate for manually unless I'm not getting the point.
You have Team 1 and Team 2 clearing Kara and sometimes on different schedules. So you schedule 2 sets of raids and thus people in the guild show up with less than 100% attendance. The simple factor is that is they show up with at least 50% attendance you should be able to deduce that they made 100% of the Kara raids. With 1 or the other groups. The difficult part of using the system as is would come to adding tracking for the 25 man raids with it. At this point the numbers will skew slightly but then they won't show up accurately if you have teams allocated for tracking attendance for Kara and then the 2 teams combine with 5 floaters for a 25 man.
If you look at your dkp menu you have the link that says Raid Analysis. If you click this there is an option to show by Destinations. As long as you only select the Karazhan Bosses as destinations you can then use the 50% = 100% idea to calculate raid attendance for Kharazan. Then all other 25 man raids can be looked at on the normal 100% = 100% basis and doing a little math would allow you to see a true attendance.
Taking a gander at the custom column option it might be possible to do this as a formula if Chops could make variable to use based the destinations or destination zones.