Clouds altitudes in custom weather are correctly using AGL. Just did a test at KDCA, setting up bottom at 3500 feet and it was as expected. Maybe you forgot to delete a lower layer ?
This thread is related to an issue with clouds altitude, using Live weather, after METAR implementation (SU7). Since it is still open but I don’t see clouds starting from the ground as it was the case right after SU7, I am wondering if it has been fixed in a posterior release (I have never seen a fix listed in any of the release notes) or if devs are still looking at it ?