I don't think my plugin (outdated now, I think) will help you with what you want. It was intended to ease some testing a while ago, when Bootstrap was new to web2py, if I recall correctly, nothing else.
If it's just the Bootswatch theme that you wish to apply to a welcome app, simply substitute the Bootstrap files that are included with it, there is nothing else to it. If you have problems doing so, please open a thread on the user list.
Regards,
Ales