I think it makes most sense if the open directory dialog pops up first.
All other solutions IMHO have the risk to be overwhelming, and the risk to suggest this might be a "classic monolithic IDE with overcomplicated settings" scenario again. By having just a simple directory open dialog show immediately & at first the user is kind of primed this is a more modern workflow, and then when a follow-up settings thing shows up *but with everything already filled out* it is way more obvious that touching anything else is optional, and that geany is quite happy to proceed without me bothering with more than just having specified the folder. I think that would not be obvious if I was greeted with a base folder + name + whatever dialog to start with, with nothing filled in yet.