no incompatible driver messages here, and my Gearbox patches can be edited/saved as per normal (as prior to upgrade).
I am running Gearbox v3.72.0 (which I believe was the final release) with the Line-6 driver ( v7.3.8). Seems the difference is that you have the POD X3 Pro, I have the UX2.
I did notice that under Gearbox / View / Hardware Info it states :
USB Connected: YES
Driver: Not Installed <----- seems odd ? but its thankfully working anyway
USB Firmware: v1.01
Maybe slightly off-topic - I still have an issue that Gearbox (v 3.72.0) will not save its preferences and always launches with the default "American Punk" patch. Just an annoyance rather than functional issue, but I had this on Mavericks, so it is not related to upgrading to El Capitan. I have checked the app preferences and I definitely have Read & Write.