Sorry bobc50 as your questions gone by without me noticing earlier.
Do you agree with my assessment
As it stands right now with the information available then that could indeed explain the behaviour as you witnessed/experienced it. Especially if you are not quite sure if you used the check mark for saving your options as default and you did so indeed.
Short of changing my approach, which is based on my need to compare changes to prior versions, do you have a suggestion on how to keep this from happening going forward?
Other than the suggestions already mentioned, not really or that I am aware of.
Setting default options is something I personally do the moment I start a new Lazarus installation for the second time (I use the first time to check/verify other settings and behaviour and to make sure I did not messed up with my startup scripts/shortcuts). I then let Lazarus create a new empty project and go through all the compiler settings one by one till I'm satisfied, press the check-box and save these settings to be used as default. Then I close the empty project, create a new one and check if the default settings are indeed configured as intended for the new project and compile a first small test example with those settings.
I usually never touch the default settings again unless there is some kind of new feature that I want to try out and/or to see if it would beneficial to use it as a default setting and/or to "play" with it.
In the case were I truly want to make drastic changes to my default settings (very rare, in practice almost never usually because there is a new release before it even comes to that), I make a backup of my previous default settings first so that it is possible to revert the changes.
But that is easy for me to say because I've used FPC/Lazarus for quite some while now to know what I want the default compiler settings to be. That might not be that easy to do for someone who is new or fairly new to FPC/Lazarus.
Lazarus always provides you the option to start anew with using another (empty) configuration directory so you can't really go wrong there other than it takes time to re-configure everything.