How do you have your MBOM/MID structured to facilitate the 99 phantom limit in SAP?

It seems like an impossible task to obey the 99 phantom limit while still following the best practices of a "flat" BOM.. And then when you add variant content into the picture, it becomes even more impossible!

How do you manage the MassNs/Kits -> ERP limit of 99? Leave everything completely flat with no parents?