@Grey Roger also added an installer toggle for the yellow/ochre paint schemes.
Did I? I don't know how to do things in installers - I thought the toggle was your work. What I did, after
@Armada had changed
HMS Victory to a more realistic colour, was to repaint the entire Napoleonic British fleet in the same colour. Personally I'd be happy for some ships, if not all of them, to have both dark yellow and pale cream versions available simultaneously rather than choosing one or other at game installation, though that would mean duplicate models for each ship which has both colours. The dark yellow versions could also be shared with France and Spain, who also used yellow schemes in addition to the red schemes currently in the game.
And of course, the new
HMS Indefatigable could then also have pale cream, dark yellow, French light red and Spanish dark red variants.
Actually, somewhere in one book I ran into a description, that various RN ships in early 1800s sported yellow, ochre, and even red paints in the same time, depending on what was issued to them.
Ships were captured. If the ship had previously been in French red, it would still be in red while in British service after its capture, and they might not have bothered repainting it. Also, the ship's paint scheme was largely at the discretion of the captain. PoTC's uniform national schemes aren't realistic in that regard, but in PoTC, each colour scheme requires a whole new copy of the ship model. CoAS has an advantage here in that ship texture files are in folders specific to that ship, with three folders per ship, therefore up to three different colour schemes without needing a whole new model. (Mind you, I don't know how CoAS actually uses those folders.)
Having said that, I would imagine that while
HMS Indefatigable might have had the captain's choice of colour scheme while she was still the original 3rd rate ship, she'd probably have been repainted into a more modern, standard scheme when she was refitted and razeed into a frigate. (Of course, her new captain might then have had her repainted to his liking.)