Stan you did it again! Thanks for the help. I had multiple materials.  When I removed them, I proceeded to have some model encoding issues which resolved when I deleted the constraints. The error I was getting was: XmlParseEntityRef:NoName I know that is something to do with how Blender set up the XML data in the DAE itself, but idk. Deleting the constraints worked... Anyway, thank you very much for your help, the model is showing up in game!! 

See https://gitea.wildfiregames.com/0ad/0ad/wiki/ExportingErrors Either you have loose vertices or multiple materials, and neither are supported.

Transparency should work in baking. You're right about variation, though

The 'olive tree'

Sure, but the trees are transparencies and have random heights.