'Soft cap' as its usually called is actually referring to a bonus not a penalty. It was meant to give smaller ships an edge against super giant ships by giving them a lot of extra power with just a few blocks while larger ships will only get the normal power/block after they hit the limit of 1mill e/sec. However docked reactors have kind of broken that idea.
Only way I can see to 'fix' docked reactors would be to remove the bonus, which individual server admins can now if they so choose through the block configuration files. Not like anyone would actually do that because it would break every non-mega ship build ever made anywhere besides that server.
Simplest way I've seen to reach the soft cap is 1x1xAnyLength strips of power reactors, alternating power storage in between the strips.