You can not system transfer across different region consoles. eShop servers are used during the process and it would reject the request even on region swapped emunand.
As for me, my plans are to just system transfer my 10.5 o3DS emunand into a 10.5 sysnand on n3DS. Because my n3DS will be nand modded, this will make the process easier. I will likely upgrade to a 64GB MicroSD card as well so I won't have to worry about swapping the cards around and having to worry about emunand being on the wrong card. Hopefully I can just chose the move content over with a PC option.
My current SD is a MicroSD, so I may tell it that I can physically insert my SD into the n3DS. Since my n3DS will be on 10.5 sysnand (temporarily at least) I won't have to worry about the reboot procedure. Once done, I'll use my NAND mod to copy the sysnand over to emunand once the process is complete. Then I'll manually transfer the movable.sed and system save games from my o3DS sysnand so I can get working NNID on both emunand and sysnand just like with my current o3DS and the nands will remain unlinked to each other.