The headline is completely bogus. The author switched both the filesystem from HFS+ to APFS and the Meltdown patch was applied. This effect cannot be attributed to just one of them without further testing.
From what I could observe, applications taking the most serious hit are electron based (like VSCode, that went from smooth as silk to mildly sluggish) and Safari.
Docker on mac has also taken a hit, although I couldn't quantify it objectively.
I suppose the same applies to desktop applications. Most use a large executable with maybe a few dlls. Electron and Python applications that ship as source or bytecode will be much more affected.
And also that the raw, combined difference was 4x, not 3x?
Yes, syscalls are expensive and most likely became very expensive with the Meltdown patch. Even more so on OS X, where filesystem drivers are running in their own process.
I am not arguing against performance drops due to both Meltdown path or APFS, but I do not think your data shows the conclusion you are using in the headline.
Or the article.
Or the referenced (linked) article.
Seriously: a rebuttal of what you wrote is easy, but amounts to rephrasing the article.
> As part of the upgrade process, the macOS High Sierra installer will automatically convert an SSD to the new APFS
https://blog.macsales.com/42884-is-it-possible-not-to-conver...
> The headline is completely bogus.
One of your statements is therefore bogus.
However, it is then also assumed that this 20% performance penalty between HFS+ and APFS is going to be flat no matter which block size is used. I don't think this is a reasonable assumption.