Is there any actual benefit of leveling a follower that just runs your profession buildings and is normally not used for any missions? Does the Bonus he gives to that building increase or is it the same if he is Level 90 instead of 100?
Yes there is benefit. From wow-professions.com:
...you can assign a follower with a profession perk to your level 2 garrison buildings for an added bonus. One bonus is that you have a chance to get 1 extra resource from your work orders. The chance for getting an extra resource is only 50% if you have a level 90 follower, but it will increase to 100% when you level your follower to level 100. For the Mine and Herb garden, the bonus is that you will get 8 herb/ore from your work orders instead of 5.
I cannot now find the reference, but I believe it's not either/or; that is, the probability of getting the second resource isn't 50% at level 99 and 100%, but scales based on follower level.