Legally it works like this:
1. The EU issues a directive. Directives are not directly binding (some gray areas have developed over the years) and must be implemented by national legislatures into national law. The directive is the base line, national legislators may go above and beyond what the directive calls for.
2. In Germany we have implemented this directive (as well as "my directive", that's why I claim to have some knowledge about this issue, as well) in the "Produktsicherheitsgesetz" (Product Safety Act). You can find a translation here: http://www.bmas.de/SharedDocs/Downloads/DE/PDF-Meldungen/pro...
3. The law enables quite a few ministers to issue regulations that deal with specific things (in my example: the Ninth Regulation deals with machinery safety).
Those regulations usually refer back to the EU Directive, incorporating it partly.
For example, in the Ninth you can see (http://www.gesetze-im-internet.de/gsgv_9/__3.html) that some requirements are basically just worded as "must meet requirements A, B and C from 2006/42/EG" or "must provide documentation as per Annex I of 2006/42/EG)".
4. Law and Regulations must be obeyed. Not some "EU law". This law. And only this law.
The key insight is: how you fulfill the requirements is up to you. Also, the burden of proof that you fulfilled those requirements is yours.
5. Because those requirements are rather vague and abstract, and this burden of proof is not easily met, the law provides for some "convenience avenue" (well, and because that's the idea behind the EU's "New Approach"):
You may demonstrate that you meet the requirements of certain applicable standards. If you do this (and you still have the burden of proof here!), you are automatically assumed to be in compliance with the law and the regulations.
That's the so-called assumption of conformity.
6. That's where your linked table comes in: those are standards that are "harmonized under the Directive".
If you find a standard that's (partly) applicable (you may not use a nuclear reactor standard to claim conformance of your children's toys...) on that list, you may shift your burden of proof from the law and the regulations to the standard (as far as it's applicable).
7. So far it doesn't sound very exciting. You just swapped one set of requirements where you bear the burden of proof with another set of requirements where you also bear the burden of proof.
The thing is, those standards are tailored to your field, so they are much more practical and manageable.
And the real kicker is this: you can get certification by TÜV, BG and other "notified bodies" provided for by EU law, that you met the requirements of the standard. You probably won't get TÜV or BG to certify that you met the requirements of the law itself.
8. Okay, but isn't that "incorporation"?
No, it's not. Not legally. And not practically.
First, remember: you have to follow the German law. Not some Directive. The latter isn't directly binding to anyone, except the national states insofar, as they are required to implemented it.
The decision which standards are "harmonized" and thus invoke this assumption of conformity lies with EU organs, not national organs. So there is a real division of authority there.
And, most important: you're always free to disregard any and all harmonized standards. If you feel good about meeting the requirements of the national law and regulations without the help of harmonized standards (and in some fields you mostly have to do that anyway, because no really applicable harmonized standards exist), you're free to do so.