Why does the author put so much effort into testing VMs? Bare metal installations aren't even tried, so the article won't represent more typical setup (unless you want to run in cloud, in which case it would make sense to test in cloud).

If given the choice I'd never run anything on bare metal again. Let's say we have some service we want to run on a bare metal server. For not very much more hardware money, amortized, I can set up two or three VMs to do the same server, duplicated. Then if any subset of that metal goes bad, a replica/duplicate is already ready to go. There's no network overhead, etc.

I've been doing this for stuff like SMTPE authority servers and ntpd and things that absolutely cannot go down, for over a decade.

That doesn't really matter for benchmarking purposes. I think the parent comment was emphasizing that syscall benchmarks don't make sense when you're running through a hypervisor, since you're running tacitly different instructions than would be run on a bare-metal or provisioned server.

Because the cards were in PCI passthrough, so the performance was exactly the same of a physical system

Author mentions as much as to say that there's was some indirectness at least in the interrupts.

There are also VirtIO drivers involved, and according to the article, they had effect too.

It’s probably worth noting that there have been huge scalability improvements - including introduction of epochs (+/- RCU) - in FreeBSD over the last few years, for both networking and VFS.