Usually is far from always, though. In the run I did before last, I commissioned with the Persean League at game start, built them up to 100, and then plopped a colony, and kept doing Persean League missions and things. I had in fact -planned- to join the league... and then suddenly I don't get a polite "oh, your colony is large now, you can finally join us!" I get a blockade, angry sounding messages/hostile fleets, and they're charging a 20% -gross- income tax (my colonies would have been making negative profit with this)?! My disappointment was immeasurable, and I dropped the commission and blew up their stuff, which, honestly, doesn't say good things about me as a budding trade partner but come on, no way of negotiating anything better without at least -some- form of combat was a bit much.
It's certainly a thing that can happen, and almost acts as a weird pseudo-punishment for a player waiting a little longer or being extra prepared. Sure they have more intrinsic options to deal with the crisis because of their own preparations, but it just -feels- weird that the factions don't acknowledge any of the stuff you've done for them, potentially a lot, at that point. Even if it's just some additional dialogue about how they're under orders, or nobody gets exceptions from the AI core inspectorate (even though people clearly do, sometimes, with limitations)... That's why I agree that none of these should outright avoid crises, but they should slow them, make them more polite, and potentially grant easier access to non-combat resolutions.