Here I gave some help about this: [Help] Map Generation
Those dirt patches are actually terrain elevations, so yeah, amplitude settings will change a little of it. The same way we have multiple elevations of foot hills and mountains, we also have from plains, and the result are those patches.
From that link, the code mentioned makes sure to have only one plain elevation, nullifying those holes. But you also need to change the base height of the map to match a multiple of 5, also mentioned there. The default from temperate and desert are base 36, so just change to 39 and it will work. (if you used the code from that link)