No mod makes irrevertible changed to your system. Any registry modifications, if recommended, are made by hand.

There are mods that hook only WINAPI functions.

In Linux such kind of hacking is impossible at all. You cannot make Qt4 to look like Qt3.

No, Windhawk's rule for all mods is that they do not permanent changes, including to the registry. Disabling the mod and rebooting will erase all effects.

Both the mod's author and Windhawk's autor live in Israel, if it makes you feel more safe.

One reason is that Linux has no backwards compatibility and to maintain each piece of software in the repos, you need people. It is linear: more software requires more maintainers, otherwise the software stops to compile in a year or two.

Windows architecture is better. It is from the 1990s (ad was very advanced at the time), while Linux architecture is from the 1960s.