Here is a rough breakdown of the premine:
3.40m - gamer incentives
2.50m - dev bounties
1.25m - 10m XPY converted 8:1
0.80m - 100k atoms each getting 8 ION
0.70m - ICO
2.25m - unsold/unknown
------
10.90m
Meaning he team controlled 3.40 + 2.50 + 2.25 = 8.15m or ~75% of the initial supply.
Since then ~3.2m new coins have been generated. It stands to reason that the team got ~1.2m of that (half of the rewards 1.6m times their share 0.75) even if they didn't have any masternodes. Probably more - AFAIK masternodes take coins out of regular staking (150x20 = 3.0 million) so that makes the team's share larger than 75%.
While it's mighty nice to see the 5.9m coins now sitting in the two addresses, that still leaves 5 million of the initial supply and more than a million of the new coins unaccounted for.