@johnksellers As mentioned in the Question body, the problematic situation occurs when 1D plaintext is pasted into a 2D Input area. In contrast, when I type theta__xy into a 2D Input area then it automagically typesets.
So, where are these involved 1D plaintext expressions coming from, that you are pasting into 2D Input areas? (I'm trying to figure out whether it makes sense to consider any kind of batch process, but that doesn't make sense for all scenarios.)
By the way, the Escape mechanism in 2D Input mode activates 2D command-completion. It's a combination of Java GUI and Library-side mechanisms, so I don't think that you'd be able to locate and adjust it.
But command-completion is very useful in other 2D input situations, and I thought I might mention that here. Suppose one wants to enter a typeset 2D definite integral. In 2D Input mode simply type in the letters Int (or int) and then press the Escape key. The command-completion popup should appear, containing several alternatives including templates for both definite and indefinite integrals, etc. I find it similarly useful for entering units (I type Unit and then Escape, and then get a generic unit braced-input template). And so on.