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I'm afraid you'll have to ask Weeblr (the sh404SEF authors) about this. All I can tell you is that our router returns the URL slug in the format 1505:minimum-order-3-prints which is how Joomla! itself expects it: numeric ID, colon, alias. I don't know why sh404SEF doesn't convert the colon to a dash. Maybe an option? sh404SEF should do that since it claims to provide full compatibility with existing Joomla! extension SEF routers.

I know that they're using ATS on their site. So I'm quite confident that if you ask them they will know what you need to do.

According to Yannick there's no need to use the plugin. He pretty much told me that it's best to use the SEF router of each extension. We'll be most likely dropping the sh404SEF plugin in the next release.