Can't stop Apps from published theme (Debut) injecting themselves into draft theme (Dawn)

I’m working with a client to port their legacy Debut theme to the latest version of Dawn. This is a manual recreation with no code reuse.

I’m running into issues with the apps installed to the live theme ‘forcefully’ injecting themselves into the new theme. There are no embeds enabled on either theme; but i have around a dozen apps wreaking havoc on the DOM in the new theme as the injected scripts are forcefully loaded via this function;

Which results in all these scripts in the head of each page (and more elsewhere);

Does this have something to do with the way apps worked before 2.0 and/or before the ‘embed’ switches were introduced in the GUI editor?

Any advice? Uninstalling the apps is not an option and last resort is moving to a isolated dev store but having access to the catalog and media is very useful.

Cheers