Intake fan and exhaust fan bear different speed, does that affect overall cooling?

I see many builders uses third party fans and remove the stock fans from lower models like the Spec 03 and 05.

I have not much experience in building a new PC and trying out different things. But I really want to know if say I get a Spec 03 case and let say I replace the front with 1 H60 at the top and put an third party fan (2000 rpm) as intake below the above mentioned H60 fan/rad and retain the stock exhaust fan. Then I will put the stock fan at the front removed earlier on to the top near the rear side;

now given this setup that the each fan at the front are running different speeds, and assuming SPEC 03 fan's max speed is less than 2000 rpm, would my planned setup disrupt the original airflow design of the case and render its productivity useless?

Should I use the same fans as the stock fans of the SPEC 03?