You must provide another jbot registration in another product:
<browser:jbot
directory="templates"
layer=".your.product.CustomInterface" />
Then your interface must be something like this:
from .... import IThemeSpecific
class CustomInterface(IThemeSpecific):
pass
And you must register a browser layer for you product.
So: your new interface is subclassing the interface from the theme.
Another way is to use z3c.unconfigure.
Note: I fear that both ways will replace all of the templates inside the original folder (so I think you can't simply customize a single template).