I will dissagre with your last paragraph.
production lines are set up based on demand.
if the production is set up for automatics and you have to sneak a manual in it (gearbox, ecu, third pedal, center console, trims, bearings, guibos, the lot) and deliver it on time its a big delay unless you make a batch of manuals. Even worse with an individual colour... seems fair to me to pay for an extra and to be honest why pay for a not so great manual when you can have a top of the line auto?
I will disagree with all your paragraphs.

Manual gearboxes are much, much cheaper to produce than automatic ones, especially in the modern age where an auto is another computer with some very clever mechanical bits. A manual doesn't need hardly any electrics, or electronics. They haven't really changed in 80 years.
BMW didn't need to 'make' or 'source' a new gearbox for the G29. The Supra, which is a G29 in a Japanese frock, has been available with a manual for ages, so they just use that drivetrain. They will come in a box, complete.
Sorry, but there is no excuse for charging extra for a manual gearbox other than marketing strategy. There has been much talk of the G29 M40 being 'a better car' with a manual option by the motoring press and on car forums, and the fact that the Supra (which is the same car) has had the manual option since launch, BMW have chanced their arm and bowed to the pressure. The Z4 is due to succumb to the EV wave of pressure soon anyway, so why not? And if you can charge a premium for a cheaper product; happy days. They can put the extra profit into making more 3 tonne electric SUVs which do 0-60 in half a second (silently), for the mums' school run!