The default colors are indeed hardcoded in XTherion. They can be overridden by un-commenting and changing the respective lines in xtherion.ini.
As for the xtherion.new.ini, I think it was a backup copy of the settings or something, and not really read by the application. I don't have the sources at hand at the moment to check.
I can change the defaults for wall and rock to the ones you suggest and they will make it to the next release.
I chose the defaults because they worked well for my setup, my screen, etc. For other people the experience will be different. For example I use TopoDroid and not PocketTopo, so I don't have a conflict with the background splays.
Btw, Marco Corvi did some extra symbols for XTherion points, e.g. stalactites, stalagmites, etc. So they don't all look like blue dots. I didn't have a chance to test them and I think they didn't get copied to the base repository and to the release. I'll see if I can dig them up later...
Vladimir