I'm thinking that you should overwrite everything without root.
Then install and use SkyGo App.
Afterwards, Stop the App from Running (not clear data or uninstall it).
Then root your phone.
Then hide root and make sure you don't have any root associated Apps around (SU, TBU, RExpl, SysTun).
...now run the SkyGo App.

It should, theoretically, work as if normal. If done right there isn't a reason not to.

And if you're very dedicated you can source the mechanism. So that you can have all your Root Apps, and that you simply Stop the App from working when you're finished with it. And un-hide root and your Root Apps. When you wanna SkyGo, just hide root and the Apps again.

Or even better (but potentially harder) way would be to "crack" the file so that it also shows "false" when "root check" is initiated. This is a popular App so I wouldn't be surprised if someones done it already, try to ask around in irc etc etc and search the world wide west.