If I understand you correctly, this is not possible in the current version of Bakery. However with some programming, it might be possible to also give SKU's to Item Options. The result would be something like:
Product: T-shirt - SKU# 1345
Item Option: Green colour SKU #001
Picked together, the SKU for a Green T-Shirt could then be combined to create something like 1345-001.
I think this could be a useful feature for others. I will add it as a future request to the list at:http://www.websitebaker2.org/forum/index.php/topic,18426.msg128643.html#msg128643
Should you decide to devleop this solution, please consider contributing your modifications back to the Bakery project. Not only will this help others, contributing back can result in this becoming a standard feature of Bakery in future releases so you don't keep having to re-apply your modification when you upgrade to future versions.
With warmest regards,