My preference would be to have the Scale stick to 'Original'. It's a poor oversight from GS that resulted in this changing from sticking to 100% in AC9 to Fit to Page in AC10.
I don't know how to change the default, but as with any setting, if you select the folder that is the top of the hierarchy in the Publishing Set (which is hopefully a clone of either the entire book or at least a subset of the book), and set the Scale to 'Original' or 100% it should apply to all the subfolders (and layouts contained within them) too.
[Edit: Upon further invesigation, it appears that 'Original' is only offered for non-layout views, so printing at 100% is the correct default setting for publishing layouts, as you said.]
Cheers,
Link.