Neat concept but I wonder why the PCIe initialization delay can't be handled with an option ROM. I don't know that a fully fledged option ROM would add value but it seems like it could be a good workaround/hack to not require additional BIOS configuration or support a BIOS that doesn't allow configuration of a delay.
I've seen some option ROMs take 10 seconds or more depending on the card - hardware RAID controllers being a well known example.
i don't know anything about mikrotik's hardware development practices and don't want to besmirch them, but some places basically just fab reference designs, or smoosh a couple of reference designs together, and have a product.
it helps to keep costs down if you don't have any NRE.
I've seen some option ROMs take 10 seconds or more depending on the card - hardware RAID controllers being a well known example.