I believe there are meant to be hidden bonuses you have to search for as well, although the only one I’ve found is the armour on Atlantis.
Hopefully the POIs on the homeworld planets have special freelancer areas as well. The ones on freelancer HQ and Triton certainly don’t seem to 
I am also a freelancer. I think the loss of passive bonuses seems fairly negligible if you are an active player, larger if you are not but still of little impact. I do agree it is more the idea. Do federation also get the ingot ship hunt one that gives you an AI core at the end? If not, that is a very rewarding quest.