Dealing with save files is very hard to do right now. In most normal cases, it's not possible to do, as it's separated by which type of system the save started on. Encryption is a huge problem, and much of the reason why we can't transfer these saves; Gateway uses unencrypted saves, and a regular 3DS uses encrypted saves, so when interchanging the two, the game thinks the saves are corrupted. I haven't been able to test this myself, but I think you can do this by extracting the save using savedatafiler on a 3DS with CFW/Modified NAND installed. This will allow you to copy the save data, and hopefully inject it into a retail cart, however this would require you to have access to a 3DS with version 4.5 or lower, and go through the process of installing CFW. Additionally, you may be required to play the game on the CFW system (and I don't know if 8.x games like ORAS are even supported by that), but you will definitely need to reinstall the game on the CFW system.
Choosing which setup to play it as is tricky. On one hand, playing it through gateway makes the save unencrypted, meaning you can potentially take that ROM and use one of the card2 save tools to get your save. However, there is no guarantee the resulting file will be accepted using the "restore save" function. On the other hand, .cias can be directly accessed by savedatafiler without requiring the save to be created on CFW. But, again, even if you use savedatafiler to get your save from the digital version, there's no guarantee the retail cart will accept it like this, as the encryption might be different.
Short answer: It's complicated. I don't know if there is a true yes or no question to this. Both routes have advantages and drawbacks.
