RogertheShrubber says:
... sounds like an absolute nightmare to GM especially with PbP where pace-of-play has such a high variance ...
I only do this where I can keep the groups separate for the day-to-day events, we don't care about pacing until we have to bring people back together and then we can deal with any time-slip. But that is seldom an issue, or not one related to PbP and posting rates.
The rate at which a group posts does not really correlate to the pace at which they get things done or at which time passes, so a fast posting group might be dealing with minute by minute minutia and only pass a few hours of in-world time while a slow posting group may be dealing with grand, sweeping issues where a day passes with each post.
Of course time-slip happens, which is why I don't do this in games where they can talk to each other all the time. There may be news about happenings, and, as you say, they may end up with enemies they thought were friends because the other group messed up the relations, but we don't care about most of that till it comes home to roost.
If we know they are heading towards a meeting, we can lose a few weeks on the trip without needing to see it in detail in the story.
They do need to come together from time to time, or at least resync their 'events' else they are not really playing in the same game, just the same setting. The more it is done the easier it is, but it still does not happen after every job.