According to what Jaesen (JScones) told me when testing the beta for SH3Cmdr 3.0, the current GWX config files should work just fine with SH3 Commander.
He also said the Aircraft Markings add-on for the older v2.7 will also work with the new SH3Cmdr.
If he finds out different, I suppose we'll get it straight from the horse's mouth if such is the case.