It was certainly "inconvenient" to perform BIOS updates, but back in those days BIOS updates weren't all that common either. I don't think it should ever be "convenient" to do something like that with basic system firmware - by its very nature, it is supposed to be stable and rarely changed. Somehow this is making me terribly nostalgic... for the days when BIOSes seemed far less buggy and in need of constant change. Now, I hear stories of laptops with factory-installed crap that silently updates the BIOS in the background(!), bricking the machine when something else unfortunate happens coincidentally with it (e.g. hard reset.) I remember the ritual of "boot from a floppy to a plain DOS prompt, run the updater, and wait for a few tense seconds as it updated the BIOS".
The mention of "Thunderbolt Option ROM" makes it clear that Thunderbolt is basically an external version of PCI(e). In other words, even without being able to modify any firmware, plenty of other maliciousness is already possible - the same with any other device that has direct access to the system bus. In the same way that you probably wouldn't plug a random untrusted PCI(e) adapter into your system, you should exercise the same caution with Thunderbolt...