I do see your point... the customer does dictate how we operate, and as you say... they want to customize a standard product; not build their own!

What about this technique:

Let's say one of the STANDARD pizzas have:

HAM
OLIVES
ANCHOVIES
MUSHROOMS

Create ATTRIBUTE OPTION NAMES for each of them and make them RADIO BUTTONS.

Then, Create OPTION VALUES like this:

OPTION NAME = Ham
|_OPTION VALUE = Ham, Yes Please
|_OPTION VALUE= Ham, No Thanks

OPTION NAME = Olives
|_OPTION VALUE = Olives, Yes Please
|_OPTION VALUE = Olives, No Thanks

OPTION NAME = Anchovies
|_OPTION VALUE = Anchovies, Yes Please
|_OPTION VALUE = Anchovies, No Thanks

OPTION NAME = Mushrooms
|_OPTION VALUE = Mushrooms, Yes Please
|_OPTION VALUE = Mushrooms, No Thanks

ADD these four attributes to the appropriate pizza, and then make the "YES" button the DEFAULT button on each of them.

This means that when they call up the product, they will see that the STANDARD toppings radio buttons are all selected to YES by default... and they must click on the NO button to de-select the topping.

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UNDER that you can have your variety toppings CHECK BOXES, and they would be applied to each product based on what the STANDARD toppings are.

So... in my example above... that pizza already has HAM, OLIVES, ANCHOVIES and MUSHROOMS... so you would not have the checkboxes for those toppings, but you would have checkboxes for OTHER toppings...

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Radio YES / NO buttons for STANDARD toppings

CHECKBOXES for optional toppings