I was trying to help out, but it didn't work. However, the following was reaffirmed:
- If there's no layer stone on the map, the surface will flash in gorgeous eyesight-ruining colors and you get the pebbles and boulders made of everything at once
- This seems to be specifically related to that there has to be a stone with the tag [IS_STONE] and the layer tag you are embarking on, such as [METAMORPHIC]. The fact that the stone exists on the map does not help - you can make all layer stones [DEEP_SPECIAL] so they should be on the map but not near the surface and the surface will still flash
- Having non-layer stones such as olivine does not seem to help either
Removing layer stone altogether furthermore causes DF to crash when entering fortress mode, without leaving anything in errorlog.txt (assuming you removed all references to stone - it does note those referring to something missing if they are left in), which irritates me to no end as I would like to understand what is going on.
There's two alternative solutions. One, manually change every flashing tile on the surface into something else with dfhack. It may seem like a lot of work but you only have to do it once, and pebbles aren't that frequent. Then I would assume you can with correct modding have the earth itself consist of ONLY clays and sands with mineral veins in them. Or two, make a tileset that makes pebbles and boulders invisible. I would assume this is as simple as changing init to simple ground and replacing the period character as well as the infinity symbol with transparency. This will also change the way the fortress interior looks; you could compensate by adding background color(?).
Either way, vaporstone is an easier fix, but it's not as atmospheric.
Added: if dfhack is easily run from command line, could probably relatively easily write a script to do this for you