Thanks for pointing this out and you're absolutely right. The per capita comparison is much better, and shows Estonia's economy at 54% smaller [1] (Bulgaria makes for an even starker contrast at 82% smaller per capita [3])
Edit - As a final edit, the largest disparity across standard of living in the EU is between Luxembourg and Bulgaria, and comparing their per-capita GDP shows that Bulgaria's economy is 93.2% smaller [4]
This is still a considerable difference between the two countries and yet not everyone has fled from Estonia/Bulgaria.
The point though is that there is a very big spread in the standard of living [2] across the EU and yet mass migration is not occurring.