One possible solution here is to change the translation domain used either by libmypaint or by mypaint.
I think it would be better to change the domain used by mypaint (to, e.g., "mypaint12"), since that change would only have to be a temporary one, until the next version comes out, which will (if I understand correctly) *use* libmypaint. But of course, you'd have to coordinate with the maintainer(s) to make that happen. I took a look at the mypaint source, and unfortunately they don't have a centralized location where the translation domain is defined. (Say what you want about autoconf, but if they used it, this wouldn't have been a problem.) I think I *might* be able to make a patch, but it's enough effort (without autoconf) that I'd want to know the mypaint maintainer was interested before I bothered. Or you could change the translation domain used by libmypaint (perhaps to "libmypaint"), but that is a lesser solution, since the patch wouldn't have a clearly defined expiration date.