I was surprised to find forum posts dated 2011, which means Apple still hasn’t fixed this, maybe they do not think of it as a problem which should be addressed, and if they haven’t addressed it in 5 years, I don’t hope they will come up with it in near future. I searched for a solution and found that there are many others who face the same issue as mine. I use different machines for different purpose, and even when I forced myself for using the ‘natural scroll’ for the mouse, it creates problems when I was using my Windows Desktop for work.
Even though Apple has given separate check boxes for enabling ‘natural scroll’ in both Touchpad and Mouse preferences, but they both are linked to each others, which means if you uncheck it for the Mouse, it also gets unchecked for the Touchpad as well.