I'm a native English speaker, and I also have no idea what the author is talking about. I don't think that word means what he thinks it means. I think he is using "commiserate" to mean "complain".
You may commiserate with a team member when you both get made redundant, as a healthy example.
When a team of several engineers are all thrown under a bus by a PM, they may commiserate with each other about the workload they find themselves with, as a slightly less healthy (but common) example.
But when you, as a manager, commiserate with the team about the PM throwing you under the bus, you are doing your team and the organisation a disservice, in that you're creating an unhealthy us/them dynamic when doing so, and the other things the article suggests.
But I think you're right, he's saying employees are complaining and the boss is providing sympathy.
it always used to mean some kind of shared negativity though like many words the nuance and original meaning has somewhat drifted.