These bug reports are all for "Max FPS for High Quality PCs".
cl_loadondemand_default
no longer exists on the latest version of TF2 and causes a warning to be printed.
For some reason (I was previous on rhapsody's config) alt-tabbing out of TF2 while in the main menu causes music stuttering. EDIT: It was caused by the snd_mixahead buffer being too small. Better leave it at 100ms so it doesn't stutter while tabbed out.
This one is a minor one, but
mat_disable_d3d9ex
causes a warning on first launch (with an empty config.cfg) that a restart is needed to apply the change.
The "Enable facial features section" has convars set for disabling that aren't present in the enable section such as blink_duration. Here's the default values for this section:
// Enable facial features -- turning them on lowers framerate by 5ish%
r_eyes 1
r_flex 1
r_lod -1
r_rootlod 0
r_teeth 1
r_eyemove 0
r_eyeshift_x 0
r_eyeshift_y 0
r_eyeshift_z 0
r_eyesize 0
blink_duration 0.2 // Not in the convar list?
This is also happening in other sections like shadows (nb_shadow_dist) and gibs (cl_phys_timescale). I take it you expect the user to delete or comment out the entire "disabled" section and not just the ones that are set in the "enabled" section, right?
Maybe you should consider GitHub so people can file bug reports and see what's changed?