It comes primarily from a safety point of view. The concern is that the manufacturer has no idea of the possible handling/stability issues and prefer to ere on the side of caution.
Technically, if they have been approved for use by the motorcycle manufacturer there "shouldn't" be a problem.
Give you example PR3A was approved fit for Honda ST1100 but shouldn't be fitted to a Trophy 1200, both large heavy routers around similar power etc, but A fit is stronger/heavier tyre which you'd want on a big tourer !
You can get PR4GT but not a PR5 in GT spec, as there is apparently bugger all difference in handling/longevity from 4gt and 5.
If you stick with similar types of tyres, ie road/road etc you'll not have an issue, the worry is someone fitting a supersports back tyre like a Bridgestone S22 and a trail tyre on the front.
Don't forget that you may have to adjust the tyre pressures to optimise handling.
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