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The only reason why two nodes would not be in agreement is if one node received a block but another did not. It would not make sense to mine an empty block if you are not mining on top of a newly found block because you have already validated that the previous block was valid.
Remember dozens of farms and mining nodes spread out all over. You really want them to be in sync. Mostly because they are paying PPS.
Keep in mind in a PPLNS pool an orphan sucks but it costs the pool their fee and not much more.
For the big Chinese pools that tend to put out the most 0 transaction blocks, their miners are PPS so if the pool looses a block it costs them money because the miners get paid no matter what.
So you submit the block with 0 transactions and get the
BTC because not doing it costs you money.
-Dave