Some of these groups really mess up the sound volume of their releases in the conversion process... you have to set the volume to 150% to get a decent volume level and not all programs allow you to do that (and they probably lost more sound quality then they needed to somewhere in the process).
The encodes are made to replicate the source as faithfully as possible, generally that means not touching the audio and disabling all forms of dynamic gain (which both affects the quality, and reduces the quietness of the quiet moments and reduces the loudness of the loud moments).
I am quite certain that no audio quality is lost, as the explicit goal is to keep the audio at maximum fidelity.
Not sure what setup you are using, but most cinematic players have a way to do auto-dynamic gain. Or, if you do want a more faithful overall experience, all you really need is a better amp.
Probably because in theatre the audio often has a big dynamic range, and the groups are aiming for a "cinematic" result. (There might be only one or two loud points in the film)
