I never tried a scenario like yours that adds two uplinks into one domain because I could not answer the question which one will/should/must be used for certain connections from downlink domains. What would you expect to happen in this configuration? In my opinion, the current implementation does not support bonding scenarios and all routing decisions are based on domains, which represent IP address ranges.
Regarding the experienced behavior, I expect it to reveal a bug in ARP handling when both uplinks are used simultaneously. Maybe the ARP waiters play havoc?
are the described observations what one should expect to happen?
In a sense: Yes, we never tried this in practice and I can’t remember if the original author planned to address such use cases.
would it have made a difference if the two Ethernet ports were in two separated networks?
In my opinion: Definitely, cause this is the intended use case of the router.
Is there a way to prevent a domain from accepting multiple connections?
I did not see anything in the README. In general accepting multiple connections is what one wants