I think brake proportional Valve (or Brake pressure regulator) which usually a part of Master cylinder is suspicious.
It regulates pressure to Front and Rear brake line.
If I were you, I try to draw air from Master-cylinder side (not Caliper side).
(Bleed from connector between Master-cylinder and pipe, same way as caliper. someone keep pushing brake then you lose connector then tight. Don't forget to put towel under master cylinder to catch brake fluid)
If air trapped in Proportional valve (pressure regulator), pressure won't relay to rear brake line but only front side.
Front has two separate line from master cylinder (right and left) but rear goes in one line from master cylinder then separate at rear.
Did you noticed both rear brake dragged when it's hot day ?
Because when air get hot, air expand and pushes to caliper and drag but not respond to your pedal.
(calipers don't respond when you push pedal, but it's pushes calipers by itself even you are not pushing pedal, when it's hot because air expand)
Sometimes, seal get old and lose pressure for only one side (front or rear).
if this happened after you did brake job, or you notice your brake was vapor locked (too much brake on hot day then brake fluid boiled), maybe air bleed and whole fluid change may solve.
if you didn't have any unusual activity but it gradually losing pressure to rear, I suspect master cylinder (proportional valve seal).
Sorry I don't have exact e46 master cylinder diagram but basic diagram, hope you can understand what I am talking about.
Picture shows "leak" but this case "Air" in somewhere in pink.
or lose seal on rear piston.