Pelo menos na versão 4.2.0.11, parece haver essa opção
$ skype --help
Skype 4.2.0.11
Usage: skype [options]
Options:
--dbpath= Specify an alternative path to store Skype data files.
Default: ~/.Skype
--resources= Specify a path where Skype can find its resource files.
Default: /usr/share/skype
--secondary Start a secondary instance of Skype.
--disable-api Disable Skype Public API.
--callto
skype:?
These commands allow Skype links handling.
--pipelogin Command line login. "echo username password | skype --pipelogin"
--version Display version information and exit.
$ skype --version
Skype 4.2.0.11
Copyright (c) 2004-2013, Skype
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