Although TBH I am not 100% sure of the exact way things go. Having said that essentially AFAIK it goes like this:
the plan is applied (hence why if you wish to install from a non-standard repo you need to do that with a conf.d script)
the overlay is applied
the conf.d scripts are processed (in alphanumeric order)
From my own experimentation I am pretty sure that the overlay is applied first as I have used it to add non-standard repos (which I have installed from in a conf.d script). However I note that Alon and Liraz always seem to add repos and apt preferences from conf.d scripts rather than add them as overlays. I'm not sure on their rationale but I have tried to follow it. OTOH I have always added inithook scripts to the overlays. To me that makes more sense...
I think you pretty much have it! :)
Although TBH I am not 100% sure of the exact way things go. Having said that essentially AFAIK it goes like this:
From my own experimentation I am pretty sure that the overlay is applied first as I have used it to add non-standard repos (which I have installed from in a conf.d script). However I note that Alon and Liraz always seem to add repos and apt preferences from conf.d scripts rather than add them as overlays. I'm not sure on their rationale but I have tried to follow it. OTOH I have always added inithook scripts to the overlays. To me that makes more sense...