The expresses are scheduled on a specific line, either Main or Bergen. While it has happened for an express to be routed along the line which it is NOT scheduled on that is quite rare. As you pointed out scheduling of the locals is the major culprit. Even though there are 4 tracks between Secaucus and Ridgewood Junction (not Ridgewood station) they are effectively four local tracks, not not two local and two express tracks which is what you would find commonly on four tracked lines where all tracks are next to each other. On a four next to each other tracks the locals run one after the other on the two outer tracks (usually), but here because the two lines diverge forming two "separate sides" there are locals on each of the four tracks in order to serve all stations. For the most part that precludes overtaking of trains -- while it happens, it can rarely be done because it involves running "wrong" rail between at least two interlockings and doing so means that opposite direction traffic must wait or be non-existent for the "side" in question(Main or Bergen). The only other way to run the expresses is to let one express go, then send the local immediately after it and not let another express chase it until enough time has passed, so as to guarantee that such follow up express would not catch up with the local. The best example of that is the afternoon peak: there are 4 NJ semiexpresses to Radburn or Ridgewood(the first semiexpress in the schedule is a Main line train) about one every half hour and the locals are soon after them.
There are a few overtakes that happen in the three track section between Ridgewood Junction and Waldwick. For example, 61 overtakes 1171 there. Just from looking at the schedule, running "wrong" rail must happen in the segment between Waldwick and Suffern -- for example, 44 seems too soon after 1148 while there is no opposing moves (on the public schedule, I do not have an employee schedule with the deadhead moves).
The scheduling on the line is undoubtedly complicated by the need to run the locals on both "sides". The line in its current configuration is probably close to saturation in terms of expresses at peak hour, not that there is need for more at current ridership levels. Eventually Metro-North might end up needing to pay NJTransit to triple track between Waldwick and Suffern if they decide to run hourly express service, but that is probably decades away.