My first question would be if you are using cleats and are they the same for both bikes? Having your feet “tied” to the pedals can change the angles of your normal legs movements which may not seem significant at first, but become a major problem over long distances/time.

no iam not using clip ins. plat form pedals

Different seat heights could cause knee pain. Or the position of the seat (fore and aft) relative to the bottom bracket and crankset. Try moving the seat post up or down in small increments. Generally pain in the front of the knee could indicate a seat that is too low and pain behind the knee a seat that is too high. Or try moving the seat forward or back in small increments.

Dunno because everyone is so different, but most people that that you will hurt your knees if your seat is too low. Too high and your hips rock. Bars too wide and your shoulders hurt. I was fortunate…bicycling fixed a knee problem (hit ice while skiing) for me. I think the muscles pull the bones straighter and it fixed it. That said…float in pedals can be an issue also.

Not sure what you are using for pedals, but you might need more float in your pedals. My right tib-fib tend to go out (messes up my knee and ankle) when I don’t have enough float. Instead of wearing out the bike, it starts wearing me out…not what I had in mind, but I didn’t know enough about my pedals when I first started.

Try measuring the exact ergo set up of each bike and compare them. The measurements I use are:

1) center of BB to center-top of the seat.
2) center of the BB straight up to an imaginary horizontal line from the seat and then from that point to the center of the seat is the measure.
3) front of the seat to an imaginary vertical line from the handle bars where they mount at the stem.

Since I assume your road bike has drop bars and the mountain bike has straight bars there are some differences there but still the measurements should be close. An ideal mountain bike setup will differ a bit from a road bike setup though.

As far as the professional set up the issue can be they set up a theoretically ideal road bike position your body may not be adapted to (yet). You need to adjust it to your riding style. Plus some of it, especially muscle pain, can be your body adapting to the position. That takes several weeks of regular riding to make that adjustment.

A clip in pedal with a cycling shoe is very helpful and important to pedaling efficiency. The hard soles waste far less energy being compressed with each pedal stroke.

Also, check your bike’s crank arm lengths. Many have crank are lengths too short for the rider. Depends on your hieght of course.