I think he has some iffy premises. I'm not certain, but I guess pthread mutexes probably use userspace mutexes under the covers. If they don't you could select a library that does. Grabbing uncontended mutexes should be basically free. It is definitely not a good idea to write all your own abstractions, as he suggests, unless you have a really great understanding of the issues involved. You'd probably still get it wrong sometimes even with that.

Affinity is definitely valuable, but I don't think you should need to disable interrupts for most applications. I'm not even sure if it is generally possible, since interrupts are sometimes used to swap pages or notify the kernel that a page isn't mapped or that a blocked resource is now available. The reason affinity is valuable is not because of kernel interactions. It's because of NUMA and cpu cache swapping. Affinity can prevent thread migration, which is expensive mainly because data also has to be migrated or else accessed in a less efficient manner. Likewise, make sure that if you dispatch an asynchronous call, the handler runs on the same core you sent the call from.

Finally, it's a common fallacy in these kinds of posts to act as if threads can't be used to do shared-little or shared-nothing-style multi-programming. They often aren't, but there's nothing that prevents it.