It's really the same issue when you get down to it. IMO the command line flags should *not* save to the settings, but override what's in the settings at start. That matches command line flag behavior in pretty much all command line programs I've ever used and I see Pd saving those flag settings automatically an anomaly.
Thank you for your point of view!
As stated in the PR, I vote we change that behavior and perhaps add a new flag like "-save" to allow saving the settings *with* the command line flags.
Or just use the "Save all preferences" function in the "File" menu, since we should avoid introducing even more command line flags.