If you are hosting the file from FileMaker server, then the first layout opened will always be the last layout opened *at the time the file was last opened in a copy of filemaker pro* - In other words, when hosted by filemaker server it never remembers the last layout opened. Solution : turn off FM Server, open the file in a copy of FM Pro, make sure the proper layout is showing, then close the file, and re host it in FM server. Took me a while to figure this out. Perhaps this helps?
I don't know if it addresses all your concerns, but the FileMakerStandards.org suggested best practice for low-impact startup layouts might be a helpful source of inspiration as you figure out how to approach this.