Some modding help

Ok so a few things:

Preset COA (so Stark, Arryn, etc COA - basically any COA in canon) is unmoddable by the method you describe (which is why you can't change its colour in game for example) all that code in the entry you found is basically telling the game for the dynamic COA system to load a particular image from the flags file and not try to change it. If you want to add a new COA you essentially add it to a COA file in the ...gfx/coa folder, then go to the common/dynasties folder, and create a dynasty and tell that dynasty to use the COA you just added (so it needs to know which of the COA files to look in and which number along of COA it should use). Then making said COA dynamic takes a while and you need to ad a bunch of triggers and add the COA to the list, etc etc. Basically if you want to give House Arryn Stark colours you would have to do it yourself in GIMP or paint etc (as luck would have it I do actually already have it for something I'm working on for More Bloodlines)

No idea on commands, my understanding is they use a hidden building or something, no idea how to change this.

You can have as many dynasties as you want using the same COA (Arryn and Gulltown Arryn already do for instance) BUT you will need to set up new triggers etc for the new dynasties to actually use the COA (indeeed the dynamic COA is actually separate from COA itself, so if you gave the starks a targaryen COA for example the dynamic system would still show a wolf unless you also changed that).

You could create a high lordship of oldstones, as it's a high lordship it would use the dynamic COA system too.