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I am using DoT, with quad9, and I made sure to have no DNS servers in system > settings > general.
I have quite a few blocklists which I use, and while everything is working it all seems fine.
I randomly face issues where unbound just stops resolving /crashes , however, in the logs , I can not see anything related to a crash. Because this kept randomly happening, I run BE on my main gateway and  I created a secondary VM with opnsense for a secondary DNS.

I;m trying to understand your use case here; why cant you have 2 instances running on 2 different ports ? These are servers right ?or are they clients ?
If they are servers, just give different ip:port  to each of the clients and they will automatically connect to your different WAN interface as they are currently doing.
If they are Clients and you are connecting out; you can simply create a load balancing gateway where you prefer 1 connection over another for that ip  that you are connecting to. In both cases; from what i understand your use case should work. Unless there is something else you want to achieve.