I have the 4000NEX with aviv-U260 navi add-on, and use iPhone 5s with AV Adapter for App Radio. 

Here lies the problem, If I want to use app radio, it basically disconnects the navi unit. Even tho the navi unit has its own rgb port in the rear of the HU. I installed a hdmi switch, allowing me to turn off hdmi signal from AV Adapter(which is integrated in my iPhone mount on dash) so i don't have to unplug hdmi every time i want to use navi. When I have the hdmi hooked up, the Navi icon doesn't show up anywhere on the screen, when i do not have hdmi hooked up, the Navi Icon shows up in green where the app Radio Icon normally shows up.

I just wish pioneer firmware update will eliminate this annoyance, Which means, added icon for CarPlay, Navi, and AppRadio. After all, the Navi is made by Pioneer, for this HU. Nowhere did i find where they say you cannot use avic-u260 in conjunction with App Radio. 

Considering these head units can't even access Bluetooth audio at the same time as app radio or USB iPod connectivity, I find this unlikely.

While it isn't the case with the 4000, on the 5000 that port is used for the app radio connectivity for the iPhones with a lightning port, and on all units if you have a 30 pin iphone, that port is used that way as well. As such that port is in appradio mode whenever any iPhone is requesting it.

It honestly is pure idiocy that these radios can't do two things without unplugging and restarting the entire system.

I dont mean to be negative here to the OP and I certainly understand why this is frustrating but I can almost guarantee Pioneer wont fix this. Just dont want you to hold hope where there is none.

I don't take it as negativity, but being realist. I still love the unit.