I personally have an ASUS router (RT-AC66U) that has VPN functionality that I do not use. Do you mean if I could VPN into the main AE set up as a router that then when I ran Airport Utility remotely from here I could see both the main AE set up as the router and the AE set up as the bridge?
That will work just fine. You will have to rearrange the network.
Cable modem--- AC66U---AE1---AE2
If you do not want to use the Asus for wifi that is no problem .. turn it off.
PPTP and OpenVPN servers are available.. usually the first one to try is PPTP which is easiest to setup and has easily available clients.. Asus do a good job.. but you might find the Merlin firmware works better.
See this page for more info.
http://www.asus.com/us/support/Knowledge-searchV2/?keyword=ASUSWRT%20VPN%20
I am happy to setup a vpn for you to access.. I have a very similar setup to the above.. and can setup OpenVPN or PPTP and you can have a trial at accessing it.. there are two AE routers setup as I suggested as well..
Send me an email.. roll your mouse over my name and the email will show.. we can arrange it when we are both online.
Just so you know why this works.. your computer will receive a new IP from the Asus in my network.. placing it over the vpn tunnel in the same network as I am in... and therefore open to any resources in the network.. except some things like names won't usually show up.. it will need to be handled by IP address.
You can then test how airport utility works over the link..