westfw:
get the Arduino "libraries" set-up as true link libraries.
Is there a reason to do this in addition to the "-ffunction-sections" "--gc-sections" options?
Mostly just to avoid the unnecessary recompilations, I guess. The "make" way of doing things is to rationally manage a build so things don't get recompiled unless they actually need to be, after all. So a little bit of a speed of build benefit, and probably a bit more satisfaction that things are being done "properly", if you will. There is some happiness to be had in having a sharp set of tools. But as you point out, perhaps no difference in terms of what the .hex ultimately looks like.
westfw:
Do set the Arduino IDE to "verbose" mode and watch what it does before you go off trying to create a makefile from scratch...
Good advice -- I will certainly do this if I proceed. But in the near-term, I'll go with the system as it is, in order to get a bit of confidence it has indeed covered all the bases as well as it appears.