Yes, but it's not recommended.
Quantity Breaks Now and Wholesale Now auto-install in, and add code to, your currently published theme.
They also save settings in to a helper file we include in your current live theme.
It is possible to copy code over to your unpublished theme, but any changes you make in the apps would once again get saved in to your current live theme and you'd need to copy the helper file over again to your unpublished theme.
The situation is even more tricky if you didn't want the code in your current live theme as the apps check for the code each time you login and, if the code is not found, add the code back in to your current live theme.