There's an important distinction though. Windows is a de facto monopoly in the sense that almost every PC built has Windows installed on it, but not all PCs built are by Microsoft.

Apple has always maintained that the physical object is tied to its software and vice versa, on the other hand. They have no interest in running on the vast majority of mobile devices (android handsets control the majority of smartphone market share by a wide margin). The only exception to this is when Apple is selling services, in which case they let you run iTunes on Windows and Apple Music on Android. It's not like you can install macOS or iOS in any supported method on a non-Apple product.

This is an irrelevant argument in a perspective of monopoly and its market definition. Even Apple itself gives a list of competing web browsers in the iOS ecosystem to refute App Store monopoly arguments, but this also strongly suggests that iOS and Safari are separate products and browsers in iOS itself is a competing market.

The only possible argument is that iOS is not in a dominant position in the smartphone market thus Apple cannot exercise monopolistic powers. But people doesn't change their phone because of web browser engine since its prohibitively expensive for this purpose. The result is that an Android phone doesn't work as an alternative for iPhone, thus iOS can be defined as a sole market for browser products (in terms of monopoly of course). This could've been solved if Apple allowed installation of other OS in iPhone, but they've made their choice a long time ago.

The key difference being that Microsoft was found to have market dominance and using that position anticompetitvely.

This. It wasn’t Microsoft having a “monopoly” (quotes because they weren’t by definition a monopoly), but then being anticompetitive.