Distance, relevance, style. Those are the big three reasons I see.
Distance: Not in the "it's too hard to have meetings/exchange ideas/etc" sort of way, either. I'm Head of Plot in Seattle, and live in Corvallis, Oregon, about 200+ miles from our games. Most of my team lives between 1 and 6 hours from each other. We have regular meetings via Skype, collaborate via email, and write almost everything on a private message board. Getting a team to work together across a large distance isn't an issue for us, so I'm sure it can be overcome on even a national level.
What
is an issue is chapter location. I play in two chapters regularly, Oregon and Seattle. I run plot in Seattle, and I PC in Oregon. I've played long enough in Oregon that I'm one of 'the main guys' that tends to be 'in the know,' 'in the thick of it,' and 'in up to my neck.' That's where I like to be, and I don't want to be pulled out of that position to run a module, play an NPC, print of extra character cards, or intentionally avoid modules that I would otherwise go on because I 'know too much.' If I was attending a dozen or more events a year, I might be more inclined to do something like that, but I only get to PC 4 about events a year, and I'd like to actually
PC them.
That said, our team has run a few things with San Fran, but I don't play there with any frequency. I wouldn't mind being pulled a time or two out of game simply because I'm not playing a character that's involved in their campaign, but if I was, I'd want to do less cross-chapter stuff so that I could keep up my immersion level. I understand that this might not be as big a deal in some of the EC chapters where you can get to 5 chapters in under 4 hours, but I've only got 2 chapters within 14 hours, so it's a bigger deal.
Relevance: Much like the national event, if you're not going to chapter X, cross chapter stuff isn't relevant to you. If you keep it to a mod or two, or a couple of RP encounters with a few PCs, it'll probably be targeted at the people who it is important to, and you might expose some people to a plot that may encourage them to head over to Chapter X, and that's fine. My rule for modules, encounters, and the like is to ensure that the work that goes into something is balanced by the total enjoyment and exposure time that the PCs interact with it. I don't spend 4 hours setting up a trap module for one player, that's a bad use of my time. I will spend 6 hours designing a riddle module that I can run 4 groups of 8 players through, that's a great use of my time. Same opinion holds here. I don't want to spend 3 hours in a meeting with two plot teams, then another couple hours of prep and setup, then a couple more for each plot member and NPC who runs the module, for a total of 30+ hours going into an encounter that only a small handful of people will care about. It's not an efficient use of time.
That may sound a little too 'businessy' for some folk, but I think it's a really good policy. That's not to say that we don't occasionally bend that rule a little, but it's served us well as a guideline thus far. Like other chapters, we occasionally build
crazy time-consuming props, but in the example linked, it
was used to entertain 60 PCs for 3 hours, so even though it took forever to build, I think it paid off.
Style: There's just some things that I don't want in my chapter, and I'm sure that every plot team has that list. Sometimes chapters are pretty easy going and let in all sorts of things, but some aren't. Sometimes that really impedes cross chapter plot, and sometimes it doesn't. It's not terribly difficult to send an ambassador, or a big bug, or whatever into our chapter right now, our campaign is pretty flexible, but that also won't always be the case. Our campaign is changing, and that's something that happens all over the alliance whenever there's a large staff change, a big plotline ends, or new rules get added in. Suddenly the cross chapter plots may not work, may end up being dealt with differently, and could otherwise be pointed in a completely different direction than one team or the other (or both) intended. While that's not always a bad thing (PCs do it all the time), a sudden jostle like that can suddenly knock things akimbo and really screw something up in an unforeseen ways that then both teams have to address, and those things could influence other plotlines that they weren't intended to or impinge upon stylistic or thematic pillars that the campaign is built on.
If, 'for example,' Deadlands calls us up and says "Hey, how do you feel about Lichy McLicherpants coming over and teaming up with your campaign's Wraith King this event" and we say "yeah sure, send 'im over!" Then suddenly the PCs decide that they're going to, I dunno, drop a True Empowered Haven of the Living on them at the last minute, and we think that it's a really cool way to kill our BBG and totally alter the direction of our campaign, but Deadlands doesn't want McLicherpants to die since they need that guy for next event (he's got to keep the Bauble of Plotiness away from the PCs or something) suddenly there's a problem. Unless they've got a plot person on the scene, they're going to have to deal with whatever we come up with for poor Lichy (which might be something like 49 Destroy Undeads to the face), and they might not have wanted that.
There's plenty of good reasons to do some small stuff, but I think it stands to reason that there's plenty of good reasons
not to, as well. Those are the big three I can think of. There's also things like personality differences, too many cooks, etc. I treat cross chapter stuff as sprinkles: They're fancy, but that's not why you chose to play here.
