https://developer.skype.com/jira/browse/SCL :
click "Audio Calls": 66 unresolved issues

Mine is https://developer.skype.com/jira/browse/SCL-471: When booting computer Skype regularly uses wrong sound devices in stead of the previously correct ones

I think at boot alsa does not keep the same order for my webcam microphone and my motherboard audio and that's the reason why I more often than not have to reconfigure the sound devices of Skype.

At least one audio call is resolved now: I've found the solution for my problem. See https://developer.skype.com/jira/browse/SCL-471.

I haven't read everything in the links you posted, but in

http://alsa.opensrc.org/index.php/MultipleCards

it's recommended that user software (such as Skype) use the real names of devices. I see the problem you describe in Skype and Twinkle, but not in Ekiga. Presumably Ekiga is naming devices in the right way. I'm guessing your bug should not have been closed as invalid, but modified to refer to the fact that Skype doesn't use the real names of devices. It's just wrong to expect users to edit config files in the way described to prevent this from happening.