Masking bits of an aircraft's texture sheet is a great way to subtly or even radically transform an aircraft. People have used alpha masking of the .dds sheet to hide guns, pilots, even whole turrets - although if part of the texture is hard-coded into the m3d you are out of luck.
This is a great easy-to-use guide prepared by Sopwith Camel, in 2012
This is a great easy-to-use guide prepared by Sopwith Camel, in 2012