I am of course for changing it to use “config” by default. The more I think about it the more it makes sense. runcommand for everything else doesn’t set default configs, but enables overriding of them on a per core / per rom basis. Except this case, where it ignores your retroarch.cfg and sets 640×480 render res.
If switched to config as I would like – I could also add an additional entry to the config editor to set the default render res in a simple way for those that were happy with 640×480 being the render res for everything.