I'm trying to study this issue on a Linux system, and the custom styles data is saved in
~/.VESTA/style/default.ini
You just gonna have to find a similar file in a userspace of your windows machine.
I have tried to change an atom color and save it as default, however, from what I can tell the new color is not applied to a new structure, only to the original one and the changes are saved in the .vesta file.
As to the isostructure data
when I made changes and saved it as default, there was a new block of text added to my default.ini file at line 953
ISURF
1 0 3 255 0 0 255 255
0 0 0 0
looks like
3 is isosurface level (I changed it from default 46.4002)
255 0 0 is red color. (Green and Blue are 0 respectively)
255 255 "opacity 1" and "opacity 2",
I don't know what first two digits mean.
Hopefully this will help.