REINSTALLED Chameleon the other night with a homemade theme, and did not leave Default Theme in Extra/Themes/. Voila, the computer booted and followed the theme selection in com.apple.Boot.plist, and I booted into my homemade theme.
Have no idea why I was continually booting into Default theme before. I suspect that there might be something in Chameleon that prioritizes Default if it exists, but, oh well. No default theme in my /Volumes/EFI/Extra/Themes folder, and Chameleon is now working for my system exactly as expected. I am happy that it is now recognizing my theme upon boot.