> So the question remains: why is the default setup procedure creating
the xorg.conf file in some different way?

Because when the installer CD starts and configures X, the "battery"
kernel module is not loaded, and therefore the laptop-detect script does
not see the battery and does not recognize the computer as a laptop and
then does not write the "synaptics" section.

For the specific card names turning into "Generic": the mapping between
PCI IDs and names is in the libdiscover1-data package, which is
deinstalled at the end of the installation.

-- 
Synaptics touchpad detection (regression)
https://bugs.launchpad.net/bugs/40503
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