I have linked my physical Mesra Rewards card to the Setel app but I am still using my physical Mesra Rewards card to collect points, do I still get the bonus Mesra points from the membership level?

You will only enjoy bonus Mesra Rewards points under each membership level when you use the Setel app to fuel at PETRONAS stations.
If you choose to swipe your physical Mesra Rewards card instead, you will only get 1x points for every litre of fuel purchased.