You're correct, basically nobody knows what will happen. That's why many people don't want a UK partner in current applications (or at least prefer a different partner if a suitable one can be found), because they don't want this risk that, in 2 or 3 years, the UK partner might have to withdraw, if the UK leaves the EU research programmes. They might not have to withdraw, too, but nobody knows for sure, so it's a risk. Hopefully by next funding round the UK's intentions/timeline will be clearer, so people will either unambiguously know that the UK will stay in the EU research programme long-term, or that it won't.
Thanks for clarifying that this is just risk estimation based on not knowing what the outcome is. There is also a risk in not including UK institutions- they have some mighty fine researchers there, so not including them might lead to a project not being approved (for lack of continental experts in a specific topic) or being unsuccessful (for lack of execution capabilities).
It's trading a well-understood risk for a one that is not well-understood, hence my comment about it being irrational.