Technically, the dataplate should be removed or modified if any of these modifications are done to the engine. As long as the engine has it's certified dataplate on it, it is suppose to conform to the type certificate. This includes mags, fuel delivery, compression ratio, etc... The list goes on and on. While most people ignore this little facet of the FAR's.
The dataplate could be modified with an "X" or something after the designator. (IO-360A1B6-X).
By the same notion, it must be operated with the designated within the minimum fuel grade limitations as well, unless modified by STC. All major engine maintainence must also be performed by an A&P (Replacing cylinders, overhaul, etc). If this wasn't the case, imagine a homebuilder buying a O-360 core, overhauling to factory specs, and putting it in his RV. He than crashes his RV (sacrilege) and sells his engine on e-bay to a guy with a Cessna, who then installs this engine because it's dataplate still says it's certfied.
Oops...
Seems a bit far-fetched, but it really isn't. I liken this to putting a different cowl on a Commanche vs. on a RV. The certfied airplane has to have an STC, the RV can just be swapped out. As long as that engine maintains it's certified status, it must be maintained and operated as such. Not many people do, but thats the way it is suppose to work.