The Quote from MSI says something like:
According to the terms of our warranty replacing the cooler is not expressly forbidden, therefore it's allowed.Should a defect occur during the waaranty period, [the cooler replacement] is only relevant. if the defect is caused by "improper handling" [original term is only used in legal documents, in this case means something like it's an electronic component that is sensitive to things like static electricity, etc. , handle accordingly, legeal definition of the term is where the debate starts... ] or bad modifications [i.e. scratching, too much pressure from the cooler, bent parts, ... as opposed to proper mounting of an aftermarket cooler]. if the card is damaged during the cooler swap, all damages are to be paid by the customer.
In non-legal terms: do it right and we have no problem covering our warranty, if you don't you're on your own. MSi says to OC damages, normally not a problem and also hard to check, only in case of extreme overclocking (DIce, LN²) we decide on a case by case basis.
To get the warranty you have to send it in with the original cooler.
The last part of the article describes the legal situation in Germany in more detail. There is a warranty as provided by the manufacturer often only to retailers, and there is a different "warranty" as described in consumer law covering retail transactions. The first to contact in case of a faulty product in Germany in always the retailer, not the manufacturer.
Lian Li V600, Asus P77Z-M Pro, i5-3570K 4.4GHz with Scythe Orochi, 140mm Slipstream 500RPM and Mugen2 115X Bolt through kit,
Evga GTX 670 FTW+ 4GB with Thermalright Spitfire and Thermalright TY-150 500-800RPM, Seasonic 460W Platinum Fanless