Boycotting is a fine way to make a statement and generally hurts any business. Anyone who thinks this is something Square is taking lightly is wrong. They drew a double edged-sword. Since fans have directly expressed they will do as much, Square has to recognize a loss of revenue. They want their product to be available anywhere and everywhere, continuing good pr and awareness of the series, selling as much as they can, but only if they can profit, naturally. They are currently saving by not having 3D translated and distributed, but they just cut out a chunk of followers, potentially forever. Depending on how long they continue to not cater to said regions, coupled with the accumulation of current and future titles that will be boycotted, they will generate a loss of figures, regardless. It's a lose-lose situation, because both parties will need to invest in eachother.
Since they are selling the title in a select few stores, there is a way for their marketing team to test the waters for future games, but it's not an accurate method since a large portion of those still dedicated may not be close to said retailers.
Now all the tantrums and the threats will certainly not help their cause; you catch more flies with honey than vinegar, but the outcry solidified there is/was a fanbase in Spain. I'm not sure any other country would have acted more gracefully.