I've had the EVO-ALL and T-Harness installed in my 2008 Jeep Wrangler (Standard key) for a few years now and it has worked without issues.
It works with the factory remote (3 lock to start, 3 lock to stop). It is setup to unlock/lock/relock when remote starting, and handles the factory alarm the like it is supposed to.
I have added a Axxess AX-RF2 2 to the EVO-ALL and setup all of the RF options using my Flash Link. I am using the 4 Pin D2d Data Cable Y Splitter. Connected wires are the Yellow, and brown/white running lights.
When I use the RF remote, it will lock, unlock, start and stop, but it will not shut off the factory alarm. So it will trip the alarm every time.
I've been through just about every option in Flash Link and and can't get it to disable the alarm with the RF.
Even with the RF, the factory remote continues to work without issues.