Anything a company does to improve its market share is a reduction of competition, the threshold for anticompetitive behaviour is higher than that. Not saying Apple never does anything anticompetitive (they do), but iMessage is a very stupid hill to die on.
Going back to the Microsoft example, Microsoft got into trouble, not because they were bundling a web browser with an OS (which would be stupid to not have), but because they were forbidding OEMs to include any other browser on pain of revoking their agreements. That is anticompetitive.
If Apple were forbidding the installation of WhatsApp because it competes with iMessage, that would be the most direct equivalent to what Microsoft was sanctioned for.
Anticompetitive behavior is a legal term with a specific definition, it does not apply to software that decreases a competitor's potential marketshare only by way of doing something a competitor could be doing on their own.