What happened to 3.6.3? Is it left intentionally free just in case 3.6.2 will require emergency hotfix, or what is the reason for skipping the number?

Scala 3.6.3 will be released. It is already cut-off and waiting for 3.6.2 (final) release before releasing 3.6.3-RC1. We don't want to introduce more confusion to the users than necessary.
https://github.com/scala/scala3/tree/release-3.6.3
Typically we aim to make a stable release before the cutoff for the next one, but in this case it took longer then expected.

The change only acknowledges fact that from that point on we're starting the development cycle for Scala 3.6.4 and allows to produce correctly versioned nightly builds.