I kept the IPv4/IPv6 settings after I installed the IPv6 only deb. It still has the IPv6 connectivity that way, but allows the IPv4 apps to work. The IPv6 connection is the default connection, so whenever I want to run GeePS, I disconnect, then reconnect using the v4/v6 connection, works no problem. Works for the occasion website that isn't v6 compliant/hosted as well.
The wifi thing will get annoying as I'm in and out of wifi several times a day. More than happy to test any updates though.