This wording implies that there is some danger of retracting the gear
above a certain altitude. Is this the case, or was this just sloppy
language and the danger is actually in flying above a certain altitude
with the gear extended?
It appears that the article is indeed sloppy in its use of the phrase "maximum altitude for safe retraction". Later the article states "However, this was above the maximum altitude at which landing gear could remain extended, at 15,000 feet,".
If I were a pilot in an unusual situation, my likely actions would be very different if I thought I had exceeded the "maximum altitude for safe retraction", versus if I thought I had exceeded the "maximum altitude at which landing gear could remain extended".
Another answer has pointed out the reasons why the manual contains a statement about the maximum altitude at which landing gear could remain extended. It appears that this pertains solely to what had been previously demonstrated in actual flight. It seems unlikely that, for a given IAS, there would be any real problems associated with flying with the landing gear extended above the altitude limit that had actually been demonstrated in flight.
Though since flutter is a TAS-dependent phenomenon, and TAS (for a given IAS) increases with increasing altitude, and likelihood of flutter is also dependent on aircraft configuration, you never know. Once you venture beyond the realm of what has been actually been demonstrated, you become a test pilot. Not recommended when flying with passengers.