Construct 2 is severely limited in this regard, but Construct 3 will be even more limiting for desktop users BECAUSE it is browser based.
Actually, Construct 3's multi-monitor support is better than Construct 2's. You can do things like open a layout view on a different monitor. Construct 2 could not do that. We hinted at the windowing support in this screenshot from one of the first blogs. We're going to cover this in a bit more detail in one of our future blog posts.
Lots of people are making statements like this which totally underestimate what you can do with a browser. We're aiming to prove that it can equal, and even exceed, native apps. It's not really possible to keep repeating this with the hundreds of posts we get every day, and people get sick of hearing me say the same things repeatedly anyway, so really the big thing is to wait for the public beta and see for yourself how it does.
FWIW, we are still focused on indie devs and making it a better tool for them - it's still probably the largest segment of our userbase. We are interested in education as well though, so we're trying to expand there at the same time.