I afraid that with out of the box Magento functionality custom options will only work on the main configurable products, not on associated simple products. More precisely you can set custom optionson simple products, but they will not be visible on the configurable product page.
I guess it doesn't really work for you since you want to make the availability of these options to depend on associated simple products.
So you probably need either do custom module or accept having more simple products.
On the bright side, having separate simple products is better to track your inventory.
Alex Levashov, eCommerce consultant at
MagenableWe help businesses to build and improve Magento stores