Does Brain track and preserve the information about the order in which parent and child thoughts were created? For example, does TheBrain track the fact that thought X was created as a child of Y rather than that Y was a parent of X?  Does it make any storage or navigational difference whether I create a thought which later has a parent added, vs. creating the parent and later adding the child thought?

It tracks creation and modification dates for thoughts and links, but as far as I can tell, it's only used thus far for the reports and for copy and pasting thoughts into other brains.

It makes no difference though as far as your question is concerned. Thoughts can be re-arranged easily, and it doesn't affect the information in the thought. Navigationally it may make a difference, but that is personal preference.
Windows 7
OSX 10.6.3
Java SE 6

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