In the BIOS you can navigate the options with the instructions provided usually in a section of the screen. If you didn't found nothing to configure of the kind we was searching for, probably there's nothing like this. The HDA intel should be the device designed to handle analog inputs and outputs (i.e. stereo jack connectors and speakers). In a friend's computer we managed to solve a similar issue by adding a line to /etc/modprobe.d/alsa-base.conf . Have a try by acting like this:
be carefull, don't erase or modify no one line and add at bottom of the file
sudo gedit /etc/modprobe.d/alsa-base.conf
save and reboot.
options snd-hda-intel model=vaio
Im' not really sure on what to give to the model option. If this don't go, try with sony or toshiba-s06. When you are editing configuration files, as alsa-base.conf is, remember: never erase lines. Is better to put a # at the beggining of a line to comment that line. This say to the program that will read the conf file to don't read that line at all. If you want to test what happen commenting the lines you said you can do it (I don't think they are the problem, this conf file looks standard), any modification should be effective after reboot. Any modification you do commenting (uncommenting) a line and rebooting should be reversible uncommenting (commenting) the line and rebooting. As always, one step at a time and carefully try to add the line.