I looked further into why my company doesn't use the MCDU's numbers and, instead uses the the numbers from the company.
Our aircraft are audited every few years to ensure a highly accurate BEW. Any add standard operating iems (galley carts, etc) are also tracked and you end up with a highly accurate OEW.
Using standard weights for bags, pax, and actual weight for cargo the ZFW starts to become less precise, but still good enough.
And I've been told using 6.7 for fuel instead of the aircraft's densitometer doesn't make for to big a difference.
Heck, we don't even refer to the MCDU's numbers to trap any WB errors.