1. It's not technically two different files, but there is different points and animations used for combat, mainly for the cannon reloading animation.
2. The Light Pinnace is an AoP/CoAS-based ship and not a VCO one, so she's not amongst the most sub-standard ones, so we can keep her.
As for the stern windows, I know what you mean and it applies to various other AoP/CoAS-based ships as well.
It is possible to remove the transparency by editing the texture files, but we'd need to replace it with something that looks "window-y".
2. The Light Pinnace is an AoP/CoAS-based ship and not a VCO one, so she's not amongst the most sub-standard ones, so we can keep her.
As for the stern windows, I know what you mean and it applies to various other AoP/CoAS-based ships as well.
It is possible to remove the transparency by editing the texture files, but we'd need to replace it with something that looks "window-y".