Very interesting, do you have any examples of how FB manages long term (2+ years out) project that involves 100+ Engineers? Are those 100+ engineers all "individuals working on their own project"?
While I was there management was trying to resolve this situation and transmit message that long term projects are impactfull and important (and strategic to company), yet they couldn't answer question of how impact should be calculated every 6 months.
Maybe by now they came up with some formula or something
That said, large cross-org projects certainly do exist. To answer your specific question, there would normally be some sort of a lead on the whole project, tech lead or PM lead or, often, a pair of those. They would meet regularly with leads of various sub-areas, organized similarly, and ensure things line up properly. Now repeat recursively until you get down to team level, where there might be a tech lead, or perhaps just a senior engineer working with a few non-seniors on their portion of the larger initiative. At this point this would get broken down into individual projects that each person owns and is accountable for. Tech lead may or may not contribute code to this project, they (and their team at large) might be involved in a bunch of parallel initiatives that often don't have much to do with each other, other than the product scope the team owns. Things like daily stand-ups don't work when everybody has their own work stream (and often multiple streams at that).
Hope this clarifies. The setup works for certain types of personalities, but I found it to be a very individualistic culture that I didn't particularly enjoy.