The MCX configurations do allow you to customize things a bit. For most deployments, the standard configuration works perfect...but if you really want to customize things, it has that ability.
Based on the setup though, the system will determine the actual BEST path to use to get to one of the Root nodes (AP with a network connection).
There is no direct configuration option though that tells the system - use the fewest hops possible. But based on the way that the algorithms work, this is essentially what will end up happening anyway when the MCX routing protocol determines the best path. If you want, you can even statically define your *preferred* neighbor mesh AP and *preferred* root node AP such that the system will use your preferred devices in the event that there are multiple options of equal value.
How I would approach this deployment:
When you begin your AP layout plan, if you have any current network drops in the area, you would first place APs in those locations (predictive survey or whatever), then you would continue with the layout/survey based on the assumption of those first root node APs existing in those spots.
From there, you would figure out where all of the other APs need to be based on coverage (determined by throughput needs, antenna types, etc). Then, if you say that you never want more than 3 hops, you look at the layout you now have of these APs and see if there are any areas where more than 3 hops would be needed to reach a root node AP. If there areas like this, then you would need to run an additional network drop to somewhere in that area to prevent the 4th hop. Continue doing this until there's never more than 3 hops needed. The challenge with this most times though is either the cost of running those network drops or simply that it cannot be done, regardless. If that's the case, then you have to get creative (create a sort of virtual root node by have a non-root node connect back using a Point to Point connection to a root node (would only help though if more than 1 hop would have been needed after that AP)