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I'm kind of in the same boat you're in, for custom programming or 3rd party applications what I've done for a work around in the past is purchase a seperate hosting and domain, uploaded all my scripts, plugins, application on there then just called them out to whichever clients site I wanted either in the header or using the <html script> or <iframe>.
Webydo would be so much better it they just gave us access to one public folder in FTP. Unless it's a informational website I still typically create my Clients website on Wordpress for these reasons.