Another one step forward, one step back post

Just noticed this on CS6 (Mac):
After I work on a project, I use ChronoSync to backup my project folder (which contains all my media and other assets besides caches) to another drive, which is an interim backup until LTO.
Now, ChronoSync is re-writing ALL my media to the back up disk.  This is a big deal when I have 120GB of media in a project, which isn't unusual.
What was taking a few seconds or minutes is now taking hours.
I can see that Pr is changing the modification date on my media when I open (or maybe save) a project.  This is what ChronoSync is looking at to determine whether to backup that file or not.
I'm not changing the media (not intentionally anyway).  Why the change in the way Pr works?  I don't see an advantage.  Can anybody (especially from Adobe) provide some insight?
I'm guessing that Pr is adding some metadata to my source files, yes?  Is this necessary?  Can I turn it off? 
If Pr is modifying my sources, doesn't this risk corrupting my media files?

Thanks for the longer description of your workflow. 
A couple of notes:
As far as the ingesting of footage coming off of cards or HDs from the shoot, I use an app designed especially for this called Shotput Pro.  It is designed to ingest footage, append filenames, copy to multiple locations and verify the data.  If you haven't already, check it out - works great on location for a smooth data process.
Time Machine will work in the same way of only doing incremental backups of what has changed since the last scan.  I guess in this way, you would come up against the same issue of the changed modification dates causing havoc.
I use Time Machine to back up everything except for the shoot reels, which would quickly fill my TM drive.  After ingesting all of the footage into my file structure, I will copy the Shoot Reels to a Drobo drive where it will be protected as a backup outside of Time Machine.  Since the original media isn't being modified over the course of an edit, I can always retrieve it and relink the files if my HD that I edit from blows up.  (Not to delve too deep into a backup discussion, but if it is really sensitive footage, i will make another copy and store it in my safe deposit box at the bank)  So, that leaves all of the other files that do get backed up to TM hourly, which are generally much much smaller. 
I also like to leave everything related to one project in 1 folder.  Your note about not wanting to have to think about exluding folders from backup is something I share - however, I do have to manually tell TM not to backup the shoot reel folder for each project I create.  I haven't found an automated way of doing this yet.
I can be more specific about how I organize my project folders and how it fits into a backup workflow, but I don't think that is what you are looking for since you already have your workflow down (with the exception of this wrench Adobe threw into the works...) Only if you are interested i will share my system.
To your original question - I agree that the way CS6 modifies all of your footage mod dates is annoying and I wish i had an answer for you.

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