I have not measured solely at specific points. I have only averaged across the listening area. I did take a look at each briefly and saw no significant change. I will look closer and let you know.
Two subs are fairly easy, but requires more gear. Provided that neither of your subs is in a terrible standing wave location, all you need to do is delay the nearest sub by the difference to show center, then set the two subs at relative levels of 70dB. This will require two channels of a device that has the ability to delay and adjust gain. Okay, it's not a budget fix. But it works great. Y out of 4806 sub out. The two sub "channels" then go into seperate channels of a digital delay or PEQ with delay. The difference in distance is added to the closer sub, then levels matched using the 4806 manual tone, the gain in the outboard device, and an SPL meter. Then the outs of the delay device go to their respective subs/amps. The propogation factor of the delay device is not factored since it affects both sub channels equally. On auto-cal, MultEQ hears the subs arrival time and level as the same, and is not confused; it thinks it hears only one sub.
Here is a great convenience feature of the 4806 (and 5805) to try. The surround User Memories (the 4806 has three) can be configured to provide an easy way to configure for movies with theatrical sound mixes (a THX mode), a second for non-theatrical mixes (a DD/dts mode with back surround as you like), and the third for multi-channel music...or however you like. Saves a ton of time and screw ups.