This isn't a question about rules, as it quite clearly states in the rules, that damage markers are removed after combat, but why have they included so many of them?

It seems like it is supposed to be permanent..

for the situation that might arise where its a big battle between two massive balls of units and the you and/or the opponent wishes for some reason to spread the damage rather than focus it.

Other than that i use them in armada!

One common strategy I've often seen and used is the Rebel player homing in on Mon Calamari and even more importantly Utupau to load up on Mon Cal Cruisers and Corvettes. There's usually one big battle a game in my experience, with multiple capital ships and many fighters on each side. Plus I suppose they could be used as placeholders for loyalty markers, but I've never been in a situation where my group has run out of them.

Yep to all above.

I also use them to track which systems I have built off of each turn so I don't lose track.

That's a great idea, I'm going to start using them to track builds.

Tracking building is a fantastic idea, top points

To add to that, what I generally do is put a damage marker on a system, then place the units I am building next to the build track, then move onto the next system. When I think I am done, I confirm I hit all of them, remove the tokens and then move the units from just next to the board to onto the board. It really helps preventing mistakes, which is easy to do in that stage.

Yup i use them for tracking builds and then for tracking deployments after that.