(The interview is referenced briefly in this thread.)
This answer in particular strike me as good to keep in mind:
What do you think is the biggest fan misconception about Gainax-- one thing people might assume about Gainax and its employees that just isn't true?
That we have lots of money. That's so not true. I remember some fans from overseas came to see our office, and since Gainax is such a well-known name they thought they'd see some impressive building, a big high-rise or something...but it's just a regular small building, they were quite shocked.
Personally, I think this means that just because Gainax will make money from their products or Eva Store, that money won't be completely distributed to them or is going to go to particular places.