But for point 2) under "IDE options > IDE startup > Project to Open or Create" why is there no option for starting the selected .lpi file? Was it intended this way?
by clicking on the .lpi file of the desired project and then right click > open with Lazarus,
Ups, lost in translation?
"starting the selected .lpi file" => Probably a lot of readers interpret as "Automatically Run(F9) that project, when the IDE opens".
You may have meant "starting
with the selected lpi file". But even then, the reader had to infer that "selected" referred to a selection outside the IDE, in the file explorer/desktop.
Anyway, if that should work, independent of the settings that you mentioned. Otherwise it is a bug.
The "Project to open or Create" setting, defines what happens when the IDE is started from it's own icon (i.e. not clicking any lpi in the file explorer).
For completeness sake, could you test this (double click an lpi) with the various options for "Opening Files from OS" (new/running/not-multiple instance)?
(Again it should work in any of them, but best to know which one may be the issue...)
And lastly, to see if the OS shortcuts are correctly set up:
Open a terminal/console and run
lazarus /path/to/project.lpi
as well as
startlazarus /path/to/project.lpi
The first one may give warnings....