Correctly sized chain with impossible too loose B-screw adjustment? I have recently changed my cassette from a 11-32 to a 11-25 (11 speed). To make the change possible, I have reduced my chain size to 106 links (53 inches) by the largest cog, largest chain ring method. For further information, my crankset is a 52-36 teeth.

When I installed my RD-6800 (SS), I noticed that even by removing the B-screw, the derailleur is never too close to the largest sprocket (largest sprocket, smallest chain ring configuration). How is that possible?

I thought that maybe I screwed up the chain sizing, but I have just recalculated using the equation and the recommended chain length is 53 inches:

L = 2*(16.125) + (52.0/4 + 25.0/4 + 1) = 52.5"


Is it maybe due to the bike or hanger design?
According to Shimano, the RD-6800 GS is designed for 28-32T largest cog, where the SS is designed for 23-28. 
http://bike.shimano.com/content/sac-bike/en/home/components11/road/ultegra1/rd-6800-gs.html
http://bike.shimano.com/content/sac-bike/en/home/components11/road/ultegra1/rd-6800-ss.html
They may have actually done something different to the body of the derailleur instead of just putting a longer cage on it. I don't know that for sure though.
Of course, that doesn't mean the GS can't work with 25. 
Your chain length shouldn't affect the B position at all. It will only affect the rotation of the cage around the upper pulley.