The reverse-engineering approach

[gjh42]

Determined people have done all kinds of things with Zen Cart. Search the forum and you will find various posts with various claims.
There is a "Sidebox Anywhere" mod designed to allow an element to display outside the ZC installation, but what you are talking about seems to be to replace the entire core ZC organization with your own.
"The Book" is an operator's manual to help people install and configure their shop functions, not a design/customization manual.
If the admitted homeliness of the admin is what you don't like about it, you can change the styling. It is about the oldest area in ZC, and is scheduled for a complete functional and presumably esthetic makeover in a future version (after essential front-end code upgrades).

[tdblanchard]

I appreciate your ears for my rants.
I think I'm finding my way around the app somewhat successfully. Sometimes I think my dog knows more than I do about code

[afo]

Dogs know everything. They're just too smart to let on.