Okay, I think I may have an answer. Rather than installing items one at a time on a fresh, OS only install, I worked it backwards on my main drive (after creating a backup).
I knew 1Password and USB Overdrive weren't a problem since I have those installed on other nearly bare partitions, and I never have the foreground app drop while booted to those.
That left all of the other third party software to look at. Particularly, anything with a driver or daemon.
I started by uninstalling the Wacom software. I hardly ever use the tablet, and it wasn't plugged in anyway. It's entirely possible having it disconnected was throwing the drivers off and causing them to misbehave. But removing those kernel extensions helped quite a bit.
However, the drops to the desktop continued. I had no other device driver/kernel extensions installed, so it had to be one or more of a handful of background processes that load at startup. I ran EtreCheck to see what those were, and which were loaded and running.
Turns out, the main culprit are all of these daemons that think they're being helpful by constantly checking their vendor's servers to see if there's an update, for no purpose other than the gleefully state, "There's a update available!", when you launch that app.
This is also why I couldn't catch them with the script above or in Console. They're up and gone before you can register what took over the foreground. The only one that would occasionally give itself away was X-Rite's XRD updater, which would sometimes remain listed in the Command+Tab list of open apps.
Some are no problem as they properly run as a background app, and never intrude on the foreground. Microsoft and Adobe are two that seem to understand how to do this correctly.
I eliminated all of these useless daemons:
/Library/LaunchAgents/
com.corel.CorelUpdateHelperTask.agent.plist
com.xrite.device.softwareupdate.plist
com.xrite.i1Profiler.tray.plist
/Library/LaunchDaemons/
com.xrite.device.xrdd.plist
com.xrite.device.xrdd.restart.plist
~/Library/LaunchAgents/
com.corel.CorelUpdateHelperTask.agent.plist
update.log (a log of updates kept by Corel)
Restarted the Mac and checked each app to see if they would automatically install these daemons or agents when launched. They didn't, and I haven't had any app suddenly drop out of the foreground since.