They probably use an algorythm that depending on how much sold the first weeks, they calculate how the sales drop, etc.
But yeah, basically the data is concocted. Nowadays we have an idea with reliable sources for the popular titles because some companies publish the numbers (Media create in Japan (every week), NPD in USA (every month), in Europe is a bit difficult due to the numbers of countries, but there are one in UK which is published every week, etc.) But this wasn't common before, so...
EDIT:
First, Intelligent Systems (the creators), despite being a 3rd party (welp, second party for the fandom), it's VERY close to Nintendo in terms of bussiness. They even have their building near to the Nintendo Headquarters (I think it was in the same street). Though Nintendo hasn't bought IS, basically it's a first party studio for them.
Also, their team is big. They probably triplified the Camelot team at that time. And they work in a lot of different projects in various genres (they're responsible of Paper Mario, Wario Ware, Fire Emblem, Wars, Panel de Pon, Pullblox...) so Fire Emblem (with Wars) was their only IP which wasn't influenced nor ordered and supervised by Nintendo.
On the other hand, we had Camelot, which, at that time, broke up with Nintendo to join Capcom in a Golf game for the Wii (despite being first designed for the PC) and returned to Nintendo with a worse team and were near to bankruptcy. They developed a game which was heavily criticised and their next Mario sport titles (Tennis and Golf for the 3ds) were also criticised for their lack of content (even now they are accused of that with Aces). If they have problems with small titles like Mario Tennis, why would Nintendo rely on them with a much more demanding title like a RPG?
Maybe FE:Awakening wasn't that profitable if they sold only 250k. But you need to understand that IS has been with them since 1984 and has developed a lot of succesful games which sold very well. Their only self-IP was in trouble (Wars was basically dead at that point), but they could be more soft with them (yeah, a bit contradictory considering if it didn't make it, they would kill the franchise lol) because they saw the potential of the team.
Also, I think it's (was) cheaper to develop a Fire Emblem title. I've never played a Fire Emblem title so my opinion could be wrong, but basically you need to design some maps and the characters, do a proper story and develop the stats for every character, like a RPG system (now probably they increased the costs because there're zones where you can move freely and there're interactive maps). Golden Sun needs more budget because the team need to design the dungeons, world map (which includes the exploration), the towns, the puzzles and their interactions with the psyenergies, the rpg system, the story, create a lot of enemies... So in Fire Emblem you need to play only in a small area and in Golden Sun you can move freely in one area which conect to other areas. Yeah, maybe with the same sales like Fire Emblem could be profitable, but it would be less... and the Mario Sport titles gives more money to them.