Absolutely! I appreciate the time and attention to this. Testing is the least I can do. If you have any other test-cases you would like me to run through, I'll be very happy to do that.
For what it's worth, it is still humming along very nicely. I thought maybe it hit an issue last evening because one of my Pi-holes got stuck in a loop trying to resolve an internal IPv6 PTR record. It ended up taking both of my Pi-holes to their knees. Was taking around 4 seconds per query to resolve any requests from my client machines.
Turned out to be a self-inflicted DNS forwarding loop with my OpenWrt dnsmasq. I forgot to modify my OWRT dnsmasq config to not forward internal IPv6 PTR lookups since it handles those locally via ip6neigh. Anyway, 15 mins of troubleshooting and >120,000 DNS queries later, I limped away from that one with a bruised ego. But, I am very happy it was not related to the changes you made for EDNS0 handling. 
** 48+ Hours Update **
Still running smoothly as can be on both of my Pi-holes. No issues to report.