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Fun fact, this is what happens when the terrain generation fails to find enough space for one of the larger forts. This is basically the "fallback fort" and is relatively rare.
We have a lot of events that are crippled due to layout, like when Rituals/Breaches, etc spawn in corridors. Back in my ye olden days of game programming I made a rogue-like and in each "map" I would spawn 3 event rooms that were large enough to host any of the random events and if a random event was triggered it would pick one of the rooms at random, or if more than one it would choose a next available room. Would something similar to that be feasible for PoE? You would just need to ensure every layout type has a tile/room large enough for events and make sure events just spawn in those areas.
We already do this for things that need lots of space, such as Betrayal Forts. But there is a limit to how many we can realistically guarantee, so for things where it's OK to sometimes spawn them in suboptimal locations, we use a different approach.
Is there a reason why Syndicate encounters in maps will always contain research and intervention and the third is a tossup between fortification and transportation? I would think that in terms of having enough space to generate different elements the research entrance would take up more than the transportation exit.
1) Fortification and Transportation have the largest space requirements (Forts are usually huge, except for the fallback fort in OP; and Transportation not only needs an exit, but a valid path of at least some minimum length in order to be fair/possible to complete).
2) Weirdness would ensue if a Transportation convoy got too close to a Fortification. If the Transportation convoy passed by the Fort, should the Fort turrets attack you, or be mysteriously deactivated? The Fort encounter can't start without abandoning the Transportation encounter, and vice versa, so either way you would have a very visible encounter suddenly failing or mysteriously not starting. And keeping the two encounters well apart would make their already significant space constraints even worse.
So basically it's just the easiest and least-confusing approach.