An interesting observation and one that has never really caught my attention. I think this is what may be happening: If you select 'go direct' to a very distant waypoint and do not select abeam waypoints, the FMC will make a simple calculation and then alter the desired course imperceptibly during the leg to achieve the great circle track. If you select the abeam waypoints option, the FMC then sees each abeam point as the active waypoint, in turn, and will make the necessary adjustments at the start of each shorter leg to achieve the desired track to the next active waypoint. In other words, it is only looking at the next leg, not the whole of the original direct route..There must be something in the software that changes the way the FMC works it out over short and long legs, but Boeing never release that much detail in the manuals or the conversion course. Maybe your technical manager can find the answer?
Personally, I prefer simply to select go direct to where I am cleared so that I can see the time/distance to that point on the ND and in the FMC. Then, with a route copy performed preflight, you can look at route 2 legs and see the original planned track and waypoints ( as you pass abeam) on the ND also. An additional benefit of doing that, is that you can turn and backtrack the overflown waypoints if necessary. They are erased once overflown in Route 1. I expect you knew that.