alsactl is used to store those setting before shutdown/logout and
restore after boot/login in previous version

pulseaudio only change the capture volume and boost of the input source
and the playback volume of those line out/speaker/headphone

http://voices.canonical.com/david.henningsson/2012/07/13/top-five-wrong-
ways-to-fix-your-audio/

you have to ask Ubuntu audio team whether alsactl is still used to
save/restore those setting

do you mean sound preference did not provide  (advanced option) GUI to
change those controls which pulseaudio won't change ? e.g. stereo mix,
playback volume of input sources, ...


control.17 {
                iface MIXER
                name 'Line Playback Volume'
                value.0 28
                value.1 28
                comment {
                        access 'read write'
                        type INTEGER
                        count 2
                        range '0 - 31'
                        dbmin -3450
                        dbmax 1200
                        dbvalue.0 750
                        dbvalue.1 750
                }
        }
        control.18 {
                iface MIXER
                name 'Line Playback Switch'
                value.0 false
                value.1 false
                comment {
                        access 'read write'
                        type BOOLEAN
                        count 2
                }
        }

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https://bugs.launchpad.net/bugs/1323039

Title:
  [To be filled by O.E.M., Realtek ALC898, Blue Line In, Rear]
  Background noise or low volume

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