In this case, I don't really mind which nation you use. I would say that (according to the submission criteria) your submission must contribute significantly to your nation's cultural heritage, so if it's important to the people of Gura and Matos only then that might be more appropriate, but if it's part of the "story" of MSR as a whole then that might be the more appropriate choice. You could also make your choice based on IC reasons, like if you think Gura and Matos as an autonomous province has the power to submit something to the Register or if that power is reserved for the governing body of MSR. Honestly, though, you can choose the nation that you want to be credited as on the Register - so if you'd rather see it listed as one over the other you're welcome to do so. I wouldn't split hairs like that when looking over your submission.
It would be different if the two nations were absolutely separate and you tried to submit something under the wrong nation, but that's not the case here.
It's really not that bad haha.