I think that has more to do with who was running the DOJ in the 90s vs. the early 2000s.
> Now all platforms are bundled with browsers and plenty of other software.
This is an interesting question. You could take it as Microsoft's argument before the DOJ being correct, that browsers become an inextricable part of an OS. Whether or not they would have been had they not included it, it seems like we can say in hindsight, of course it would have. But surely Microsoft's decision to do so influenced the way the market went.
Does that also apply to every other service and software that is either given away for free to gain traction? Does it apply to money losing VC backed companies?
Absolutely. Go look at how carnegie won the steel market by starving his competition.