The First $3000 is for only the developers, that is why it is free of royalty. But distribution fee or “Steam” royalty is not allowed in calculating Gross (Net) Product Sales Revenue. Here is an example of calculating gross revenue for a quarter of a year (the first quarter of the first year in sales life) given in the picture from this “Form” for tracking royalty dues.
It is only $50 due for the first quarter if “Gross revenue is $4000” thus “$4000 less $3000” or $1000 is the “Current Quarter Less $3000 (which is the allowed deduction per game)”. More pictures to help you calculate.