I used the "strict-order" flag to set my DNS servers to work in order per this post.
I expected queries to #1 (CloudFlared - 127.0.0.2#5552) to be more prevalent than queries to #2 (Unbound recursive only - 127.0.0.3#5553).
Actual Behaviour:
Queries to #2 were much more prevalent than to #1. To address it, I reversed the two IP addresses in the Pi-hole web interface. Now it is behaving as expected, albeit with the two servers in "incorrect" order relative to how they are functioning.
Dnsmasq handles the details of which server gets used and when, we just tell it the servers that are available via the config file. You should ask the Dnsmasq mailing list, as they have more knowledge of how Dnsmasq operates in the situation: http://lists.thekelleys.org.uk/mailman/listinfo/dnsmasq-discuss