Even with Big N closing the 3DS eShop by March next year, I want to put the information out there just in case someone needs it.
I bought a band new Japanese 2DS LL witch come with Minecraft pre-installed, first thing I did out of the box is install Luma3DS using the safe mode method to make sure to not have to open the eShop, I also did not try to update games of anything.
Then I did the Region change right away.
During the Region change process I notice there was tickets for Minecraft and the Badge Arcade Cane game witch were pre-installed, then once the process completed, I pop a Pokémon game in there and press "Y" try to update it, it failed with 009-1003 saying that my eShop doesn't match the system region.
So basically that mean any 3DS/2DS that comes with a pre-installed game, has its eShop region lock from factory because of that said pre-installed game(s) witch is also tie to the serial number of the console that let you (normally) re-install the game after formatting.
From my research over the internet and my own testing, there's realistically only "one way" to get rid of that eShop region lock and it's by registering a NNID of the original region with the console, then doing a system transfer to another console, witch remove the ties of the pre-installed game (and the region it came from) from the console, leaving it basically empty from any specific eShop region until it's open for the first time after you perform a Region Change.
TL;DR: If you plan to buy a brand new Japanese 3DS/2DS with the intention to Region Change it and still have access to the eShop (before Big N kill it completely), avoid those that comes with pre-installed games.
I bought a band new Japanese 2DS LL witch come with Minecraft pre-installed, first thing I did out of the box is install Luma3DS using the safe mode method to make sure to not have to open the eShop, I also did not try to update games of anything.
Then I did the Region change right away.
During the Region change process I notice there was tickets for Minecraft and the Badge Arcade Cane game witch were pre-installed, then once the process completed, I pop a Pokémon game in there and press "Y" try to update it, it failed with 009-1003 saying that my eShop doesn't match the system region.
So basically that mean any 3DS/2DS that comes with a pre-installed game, has its eShop region lock from factory because of that said pre-installed game(s) witch is also tie to the serial number of the console that let you (normally) re-install the game after formatting.
From my research over the internet and my own testing, there's realistically only "one way" to get rid of that eShop region lock and it's by registering a NNID of the original region with the console, then doing a system transfer to another console, witch remove the ties of the pre-installed game (and the region it came from) from the console, leaving it basically empty from any specific eShop region until it's open for the first time after you perform a Region Change.
TL;DR: If you plan to buy a brand new Japanese 3DS/2DS with the intention to Region Change it and still have access to the eShop (before Big N kill it completely), avoid those that comes with pre-installed games.