Hello,
Thank you for pointing me towards the ISRs. I checked them and they are all disabled in the sources based on my CAN configuration in Tresos.
However, I figured out the issue. It seems that the interrupts have to be explicitly enabled after init routines to be able to generate interrupts. Just setting the CAN TX and RX to interrupt mode is Tresos doesnt automatically do this.
So this, along with the linker file changes that I had done seems to make the CAN interrupts work as expected.