That's @jfb's question 
This statement is correct as long as you run both as DNS resolver (and not both as DHCP servers). It would be correct in the case of them being DHCP servers when you would have them set up with different settings.
However running 2 DHCP servers in the same LAN for the same class of IP's would be really bad practice (unless your network topology configuration would require it ¯\(ツ)/¯ ).
I think in your setup, one router and two BBBs with standalone Pi-hole installations (as DNS only) will work wonders
One thing to keep in mind:
In your DHCP server (I'm assuming the router does that) you would have to specify BBB1's IP and BB2's IP as Primary and Secondary DNS settings (so that all the clients that get an IP from it, will get the correct DNS settings).
If that doesn't work (no option under DHCP server for DNS servers), you could set it up under your WAN connection's DNS (same BBB1's IP and BB2's IP as Primary and Secondary DNS) but that will only show queries in the query log on the Pi-hole Admin interface as originating from your router's IP and not the client's IP (since the client would request from the router and the router request from the pi-hole).
You could also manually specify DNS1 and DNS2 on your clients. That will make logging on the Pi-hole a lot easier.
That would be DNS1 but DNS2 is not there for backup/failsafe only.
Some queries will bleed through the secondary DNS.
That's why if you have DNS1=Pi-hole and DNS2=Google, some site (at random) will show ads sometimes and most times, it won't.
If you Have DNS1=BBB1 Pi-hole and DNS2=BBB2 Pi-hole, you're set
and if DNS1=BBB1's Pi-hole is offline, DNS2=BBB2 Pi-hole will take the full load ('till DNS1 is back up).