That sounds very dodgy.  Time Machine, as you noted, records ownerships and 
permissions in the filesystem, so at the very least you now have a damaged file 
history, and possibly have a damaged current backup where filesystem changes 
you made have not been accounted for.  Erase the backup target, is my 
recommendation.

Having said this, your assessment of the likely consequences is about right.  
If all you wanted was file recovery, then you might fare just fine with the 
backup in its current state.  But it still makes me a bit uncomfortable 
thinking about it.

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