Of course. All things are possible given enough time and effort.
One way to accomplish DNS benchmarking is to utilize the namebench program as mentioned here. It hasn't been updated since 2010 but is available here
Another way to accomplish this on a recent version of Ubuntu (limited testing accomplished on 14.04.5) is to:
1) Download Gibson Research Centers DNS Benchmark (Granted this is also hasn't been updated since 2010)
2)Launch it with Wine with wine DNSBench.exe via the terminal in the directory you downloaded it to or right click on it in nautilus and select Open with -> Wine Windows Program Loader.

To add your custom list of DNS servers, Click the Nameservers tab and then the Add/Remove button.

Limitation: If Add System`s Nameservers doesn't do the trick you'll need to parse your csv file to obtain the IP addresses and add them (manually?) to the DNSBench list of servers.
Then Click Benchmark to complete the benchmark testing. This can take awhile so it's a good time to get up from the keyboard and stretch.
Once Benchmarking is complete you can click the Tabular Data button which will provide final bench mark results sorted from fastest to slowest.
Regarding the safety of updating your local list in /usr/share/dnscrypt-proxy/dnscrypt-resolvers.csv You can safely test updating any file on your system provided you have a good strategy. There's nothing quite like having a backup copy to insure that you can revert your changes if something goes awry. One way to accomplish this would be to simply issue the command sudo cp /usr/share/dnscrypt-proxy/dnscrypt-resolvers.csv /usr/share/dnscrypt-proxy/dnscrypt-resolvers.csv.bak