Although I think the criticism is also overblown, there's a difference: under windows, it's
mostly about look and feel. Older apps look like garbage, or are inconsistent with the current look. Take an older app and compare with an app from the store, and they look like they came from a different OS.
Interestingly, Microsoft Apps are the largest offenders, historically. They like to ship them with new versions of their common controls library, so it may take a while until you see changes in the OS itself (the ribbon being a large offender).
However, things work similarly. All the keyboard shortcuts work (unless they messed up on purpose), screen readers work, most settings work across the board (even if it makes the app look even worse). Change the color scheme, everything changes. In most cases, you can use the same API functions to interact with the controls, and WM messages tend to work consistently.
Not so with linux GUI toolkits. There has been a lot of effort in trying to make them look the same, but it's pretty obvious when an app is written in GTK vs QT or TK. Even the way they respond to sizing events change. Widgets work totally differently, keyboard shortcuts and conventions change.
It's less of a problem than it used to be, but it is still there, and it is sometimes very jarring. I don't know how to fix it, but it has to be fixed at some point.