To show just a pinch of the sausage making process, here is the area with all of the 41a files merged:
and this one has the East Asia and Burma layers:
notice that on both, if you get in too close into Davao Gulf, the units and groups cannot spawn, since your are too close. Notice also that a goodly portion of the routing there is just one group. Some routes have multiple groups using that course.
As for the supposed "gap" between the layers, using 41a and 42a as examples, 41a "ends" on February 28th, but runs until the last group comes in, which is in late April for most usually. The Convoys layer is most times several months after the "end" of the file. In the meantime, if you do not edit the RGG in the Mission Editor (doing so adds back in lines to the file), then the file starts on March 1, 1942, at 0000 hours and begins to spawn the groups, so the one layer 41a fades out, while the new layer 42a, fades in. Other mods do not alter the spawn settings of the groups, and they will usually be at least 25 hours before beginning chances to spawn, but even with that, there is a minimal gap between group layers.