He also didn't describe much of any of his technical requirements. I'd say it's a fair assumption his setup was enough different to cause an issue. Whether or not that's a fireable offense is up to the company.
He did, however describe the eventual problem: his comments table was larger than what Wordpress's out-of-the-box feature (Recent Comments) was able to sort. He had very overpowered hardware in his custom situation. It strikes me that this was an extroardinary but still within band problem that WPEngine should have eaten the cost for solving OR tell him MUCH more swiftly they couldn't.
It's a bog ordinary Wordpress multisite installation. The most exotic thing about it was WP-supercache and WPEngine have clever inbuilt logic to safely disable that when you migrate across.
I'm more curious what VPS package you had powering your stuff at Linode and how much you were spending on it each month? Reason being that 250 USD buys a LOT of server these days and it is surprising you ended up with underpowered hardware if your VPS wasn't giving you any problems.
If you're looking to upgrade in the future, you might be much better off throwing a dedicated server at the problem and setting a nightly backup to S3. Also, thank you for posting.