CE marking does not require certification to 60601-1, but if you attempted to rely on it that way, as its "Annex Z" (EN 60601-1 version only) suggests you can, the Third Editions will present new and additional problems of the very same type you are trying to avoid.
The Third Edition relies on 14971:2000, which has been withdrawn by both Europe and the FDA. Likewise, the software standard 60601-1-4 it references is obsolete as well. The Official Journal in Europe makes it clear that the Third Edition cannot be used for compliance with 93/42/EEC since it was ammended by 2007/47/EC. The Third Edition was developed before the Medical Device Directive was ammended with 2007/47/EC. The current posting at the European "Official Journal" website makes that clear.
Official Journal "(*): This European Standard does not necessarily cover the requirements introduced by Directive 2007/47/EC".
Putting the Horse back in front of the cart
Use EN 14971:2009 to support conformity with the Essential Requirments
The Risk Management standard is a great approach for satisfying the revised 93/42/EEC. You don't need 60601-1 to apply ISO 14971. Use ISO 14971 to address the Essential Requirements, and then use whatever standard(s) you choose to populate your risk analysis/risk control form. You will likely need EN 1041 to address labeling requirements in the MDD, and perhaps other particular standards, as well. I've never been able to use less than 4 standards for completing an Essential Requirements checklist, but ISO 14971 comes the closest. By comparison, 60601-1 is hardly useful at all, which is perhaps why Annex Z of 60601-1 has no table that cross references to any single Essential Requirement.
EN 14971:2009 is really right as rain when used for populating an "Essential requirements" checklist. Its ideal because CE/QMS auditors can see more clearly how the product and quality management system interlinks with Essential Requirements and "reduce risks as far as reasonably practical". For example, they can check receiving, storage, in-process and environmental controls, right where they occur, at the factory in the filed records. Of course they can check the design and development controls and like to see verification and validation reports.
Auditors doing your QMS and Technical File review will feel at home with ISO 14971:2007 being your base standard, since it is a part of the "Management System" type of standards, like like ISO 13485, 14000, 9001, etc. NOTE - Product testing labs are not not accredited for assessing managment systems anyway, since labs are accreditated to ISO 17025, which doesn't cover "managment systems".
You need to be cautious to remember that testing labs are really an extension of your "Design and Development" process under ISO 13485 if you are CE marking using Annex II or Annex V of the MDD.
If you throw all your compliance behind a standard, you more or less make the lab, and the standard your new master. For regulatory purposes, be very cautious about using the 60601-1 Third Edition. It may be "recognized" on a list like the "Official Journal" or FDA database, but relying on it as if it were the sole instrument for compliance is a really big mistake on several different levels. Your technical file or 510(K) submission will not survive careful scrutiny.
Regulations are the horse we need to saddle. Hitch your compliance to ISO 14971:2007 and drag whatever standards behind that you feel are necessary.
IEC 60601-1 Third Edition is very expensive, and not particularly useful for regulatory compliance. I know the labs are marketing this as something of a must for compliance, but many individuals I have questioned who have made that statement have never completed an Essential Requirements checklist, 510(k) submission or medical device license application. They assume more than they know. I am even more alarmed that laboratory technicians and test engineers are being asked to evaluate our Risk Management System compliance. This is not something you can measure with temperature probes, a meter and a humidity chamber. They are way out of their league if they think they can do this, and even farther outside the scope of their accreditation.
Risk management is already being looked at during the ISO 13485/CE audit, and these are legitimate, ISO 17021 accredited management system audits. I really don't think we should pay for this twice, and its really asking the impossible, for a laboratory technician to assess compliance of the risk managment system from afar. This is making "trusting" equivalent to "testing" and that is something I doubt any laboratory technician can sleep easily with. Its no wonder the Third Edition evaluations are taking 6 months or more.