1. Specifically for the first set of benchmarks linked to, they are really irrelevant because they don't represent typical workloads unless you're writing a MAAS (Mandlebrot As A Service). Node was designed for I/O efficiency, not fastest CPU-bound computations. That's exercising the JS engine (e.g. V8) more than anything node-specific. With node becoming more VM-neutral, it's entirely possible for other engines (e.g Chakracore or SpiderMonkey) to be better at other types of computation.
2. Especially in the second set of linked benchmarks, it seems the author of the article was hardly a node.js developer because they not only used an older node branch at the time they wrote the article, but they left out a lot of common optimizations (some of which were pointed out in the comments section). Even Express (which the author used) is known to not be very well optimized.
With that in mind, benchmarks are not the only thing you should be looking at IMHO. For example (for me personally), using a single language for frontend and backend is a big deal because there is less cognitive overhead when switching between the two (previously I often found myself writing JS syntax in PHP scripts and vice versa and trying to remember the APIs for different languages/platforms is difficult). There are many other benefits as well, just watch some of Mikeal Rogers' talks to get a better idea.