Unbelievable! THIS is how it should have been done from the start!
I've moved ALL configs over to the usb drive now and it easily shaves 8 secs off of boot time. The 4 raspberries screen used to sit longer. Now they are gone within 4-5 secs before loading my custom animation movie (which is still on the microsd). But everything else is on the usb drive now
I mounted dev/sda1 to /media/usb0 as I only plan on having a single usb flash drive in the system.
I replaced the following directories with symlinks:
/opt/retropie/configs to /home/pi/RetroPie/configs
/etc/emulationstation to /home/pi/RetroPie/etc/emulationstation
/home/pi/RetroPie to /media/usb0
As there are some symlinks within those folders, I simply renamed to the one I use. So for example in the download_images folder, "genesis" was symlinked to "megadrive", So I just removed genesis as all my roms use megadrive folder structures.
Now I can edit config files by simply inserting the usb drive into my windows computer and editing them, then simply pop the usb back in to see the changes. Plus I have all the theme settings, scraped images, etc all on the faster drive (usb much faster than microsd) so things like all the game images load much faster.
This leaves the microsd all but isolated to do just the core system work. I used to load my custom startup movie from USB too, but found that during startup, a lot of times the usb drive isn't ready yet so the video only played 30% of the time. Moving it to the microsd allowed it to be ready to go and plays everytime now.
I would definitely recommend doing this for power users but really I would recommend this for new users too as it is much easier to wrap your head around things when the data is all in one location.
I have not yet tried the readonly script, but I was more concerned about this part working first and it works even better than hoped! Long live the symlink!