This glitch has become my worst enemy since 1.4 came out. I've noticed some stuff about it so I may try to contribute:
1. The glitch seems to be most pronounced near ground level, up to about 150m when only a single craft is within the physics range and will gradually build up the longer you stay at low altitude. It does not happen all the time with only a single craft but it usually does.
2. When other flying craft are within physics range the glitch gets more noticeable. The further away the craft are from each other, the more Z-fighting and flickering occurs. Again, this seems to be a bit less prevalent at higher altitudes. With low separation the Z-fighting is negligible (but can sometimes still occur, especially with camera zoomed out and clipped parts (not clipped as to ensue traditional Z-fighting though, just close to each other on one or more axes).
3. As mentioned before, the amount of z-fighting when the glitch occurs is proportional to the camera distance from the craft.
4. The most interesting aspect of the glitch for me is that when ANY vessel is within physics range on the ground / splashed down, whether it be a craft or debris, all craft within load range experience severe Z-fighting. This only seems to occur when there is a combination of flying/landed craft. When the glitch starts it does not go away after the flying craft is landed (When loading both craft to runway/pad from any interface it usually does not occur.).
5. With a single flying craft, the glitch seems to greatly increase in intensity after landing, this effect does not go away until a certain altitude (150m in my case) is passed and if the craft goes under that altitude it will show up again. Reverting or loading a quicksave seems to reset this effect in these exact conditions.
6. Moving craft with VesselMover over big distances causes extreme glitching.
1-5 apply to both stock and modded installs, 6 obviously applies to VesselMover equipped installs.
All these characteristics point me to believe that this bug is caused by some sort of float inaccuracies in the data structures which hold info about the positioning of parts, almost as if the game couldn't decide where to exactly draw the part textures. Since the position values are probably some sort of floating point types, and I presume they are updated every tick of the game clock, perhaps there is some sort of a float instability which throws off later calculations, thus elevating the problem further and leading to more extreme glitching. (all these changes seem to be more or less gradual, never snappy in nature which supports this "domino effect" theory)
Oh, I'd also like to point out that these glitches sometimes occur not only between different parts, but sometimes between different sections of a single part - For example on stock airplane cockpits the windowpanes, the white hull of the part and the black window frames start becoming all "jelly-like" and clip through each other when the glitch occurs.
EDIT: I've recorded it some time ago so here's what it looks like.
This is not too severe and shows the case of glitching after landing the plane as described earlier. It can sometimes get far more extreme than that, similar to the screens provided by @Kronus_Aerospace.