I, also, have been trying to make my DNS as secure as possible while using CARP, pfBlockerNG (devel) and PIA VPN. I tried configuring the Quad9 DNS, but ended up with a large list of DNS responses in dnsleaktest.com. According to the PIA KB / support, they say that as long as you use their DNS servers (209.222.18.222 & 209.222.18.218), your DNS is running inside their encrypted VPN tunnel anyway, so SSL/TLS isn't necessary. That logic seems sound. When properly configured, dnsleaktest.com responses with only one (PIA) DNS server. This is the only configuration I've found to do so. At this point, I've given up on Quad9.
I might be wrong. Having 12 Quad9 DNS servers respond to my DNS test may be better than one PIA VPN DNS server responding. I just don't trust seeing 12+ as I can't keep track of them all and don't like that many servers logging my data, even if they are (supposedly) anonymous.
Further, I've found PIA VPN to be the only one with their own DNS servers. I spent a lot of time testing out ExpressVPN. It's supposedly faster, but I did not find that to be true. Best guess, that is just based on some 'paid for' reviews.