I have definitely heard of negotiated travel deals where the company gets some percentage of the spend back. So for instance a Delta flight might not be cheaper than United on the ticket booking site, but it ends up costing the company less. OTOH this was a Fortune 100 company with high travel spend so they had quite a bit of leverage.

Are you the same person as GP? Because that's not the same username...

Perhaps you're speaking more generally, and saying that you've never heard of shady decisions made by HR dudes? Well, I have heard of such decisions, and I doubt I'm alone.