Channel tools is neither better nor worse than panning. It does a different job.
With the master bus in stereo, when you pan a mono track (or bus) away from the centre the sound's location moves left or right in the audio field.
If you pan a stereo track in the same way something different happens. The stereo track has information in the left and right channels, which are two mono tracks, one panned hard left and the other hard right. Any information in, say, the centre of the stereo field is because they both share that information at the same volume level.
You can not use the pan control to control a stereo track's apparent centre position because in this case the pan will only make either the left or right channel of the pair louder. So the apparent centre may move, but any audio the left and right channels don't have in common will get louder or quieter depending which way you pan and this will alter the sound. For example, a ping pong delay would gain volume on one side and loose it on the other so causing a difference in volume level of the repeats but not their apparent location in space.
So if you want to take, say, a stereo synth pad, with different things happeneing in the left and right channels, and move its apparent centre location off to either side panning won't work. That is where channel tools and similar plugins come in. Channel tools can take a stereo source and make its stereo spread narrower (or wider) but still stereo, and also allow you to then move the spread's centre around the stereo field. Channel tools can do this without reducing the stereo track to mono so it still has "width", while a mono track sounds like it comes from a single point.
The easiest way to understand this is to set up a stereo track and feed it a synth patch that has different content in the left and right channels then put a ping-pong delay in the track fx bin. Or to import a stereo mp3 song. Then try panning it around and see what happens and also experiment with channel tools.
As for "unwanted" alterations made by track interleaving, all track interleaving to mono does is mix left and right channels together in exactly the same way as if you had two mono tracks and, without moving their faders from 0, fed them into a mono bus. The relative volumes of the two source tracks isn't altered. In DAWs stereo tracks are really two mono tracks, one panned hard left the other hard right, that are combined by the software into a stereo track for our convenience so we don't have to set up the routing and control grouping to keep both mono tracks operating as a stereo pair ourselves.