If there are seats available, you can upgrade onboard, at a cash cost.

The reason for the mileage denial is revenue protection. BA want to make miles for upgrade relatively difficult to stop the frequent flyers from making lots of one way upgrades into J on the night sectors. If the company wants you to get some sleep,they pay J. If not, you get a day off or whatever is the policy.

If it is personal travel then you might have to book in advance and that is where MFU comes in. The miles are your personal bribery for flying with the airline, not company trip property, unless put into your job contract.