I noticed a device was trying to circumvent my PiHole by directly accessing Cloudflare's DNS Servers. When I started blocking those connections it started flooding my PiHole Query screen making it much less useful, how do I fix this situation.
If you want Pi-hole to ignore them, what should happen with them? Should they silently be dropped (the client never gets an answer), should they silently be answered with 0.0.0.0 / :: or NXDOMAIN or SERVFAIL or ... (the client does get an answer) or something else?
I so not like if systems do something silently, this will cause issues when you forget about having configured something and then wondering half a year later why the heck some queries are not showing up. This will also be tough for the guys to debug because it is happening in the dark.
Pi-hole is a learning tool. It shows you what is really going on with your network. You can use that to find clients that are misbehaving and either fix the clients or report the unwanted behavior to the people responsible for the clients.
Pi-hole has revealed to you that a client is behaving badly. That is where you should be spending your efforts. Fix the bad client.
I don't know about this particular software, however, basing on the sole concept of that it runs on a Raspberry Pi (Linux) and hoping it is not some proprietary blob, the issue can surely be fixed. Most likely it is sufficient to open an issue ticket for this software. It may depend on a particular or a specific combination of plugins (assuming such a thing exists in there).
Other users will be affected as well so it should be fixed upstream. I don't think any actual coding by you will be required.
Another solution (without opening a bug report = without fixing the underlying bug!!) would be to create an entry for loopback in the /etc/hosts of said device. This will prevent any requests to be made to your Pi-hole at all. Quick and correct solution, however, more circumventing than fixing.