<< So I discovered that once you update firmware to install a Metal graphics card, the “option” key does not work any more! >>
That is NOT correct. I have three of those Mac Pros and the Option key works exactly the same before and after Firmware upgrade. it is not the FIRMWARE Upgrade that causes your grief.
BUT: the keyboard must be connected to a port DIRECTLY on the chassis (not on a display or other Hub) to be available at startup.
Some windows keyboards swap which key is Alt/option, usually with the Control key next to it.
¿Does you metal graphics card support Mac boot screens? many that support Metal do not support boot screens, unless explicitly modified to do so. ¿Does you new graphics card option-Boot with Mojave? it should!