Each controller has a separate message RAM(4K) to store incoming/outgoing messages, TX Messages’ timestamp, Filters to be applied on incoming Messages.
Hence the statement, “Sustain average interrupt of around 2000 messages/s on average of 500 μs/message, with a peak of 125 μs/message (8000 messages/s @ 1Mbps)” is applicable for both the controllers.
Regarding the hardware interrupts serving by CPU0 alone can be minimized by setting CPU affinity to distribute the load across the cores for load-balancing.
The cable reach might be something plays a factor in the throughput. Did you try different ones?