Are there issues inherent to running dual 6-core processors on a 2009 Mac Pro vs a 2010?
Too long to be a comment, yet not conclusive enough to be an answer - but I'd like to throw in a couple of my experiences, even if I have no comparison.
I've never had a 'real' 5,1 but I do have a 3.46GHz Westmere upgraded 4,1.

To all intents &amp; purposes everything except the front page of About this Mac considers it a 5,1.
  

I've always noticed a temperature discrepancy between the two processors - ref Mac Pro CPU temperature discrepancy - [which reached no solid conclusion] though it's never seemed to cause any problems, it just bothers my inner geek a bit.

I think the CPU fans always run a little fast, though again not enough to cause issues &amp; it can be compensated by running the intake fans a little faster.

Intake at default 600

 

Intake at 800

 

Intake at 1000

 

I also had an issue with the Security update last year - Security update 2016-003 10.11.6 issues - [which again has no actual answer] I have no idea if it's related, but I ended up not having the update installed.
I have yet to dare attempt the recent 2017 security update. I might bite the bullet today &amp; risk it.

It will run Sierra with no apparent issues, except that it's Sierra :/ [I really don't like that it breaks more than it fixes &amp; it adds no user benefit for me.]