Initialize start-up applications in certain workspaces?

Yes , thats possible using gdevilspie ( GUI of devilspie) :

Open Terminal and type the following coommand :

sudo apt-get install gdevilspie

Now open gdevilspie with (Alt + F2, gdevilspie, Enter).

Click start daemon and automatically on login .

Example here is Skype ( you should set it to run on startup ) :

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devilspie Here

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Now restart daemon and try .

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