Oh k'lin k'lin k'lin, see this is why your here, ask and you shall receive.
Now bear in mind that my S3 doesn't have a locked bootloader (int version) but I might be able to help clear up a couple of other things.
The kernel is the main "guts of the brain" of any droid version, it sets limits and stuff and holds vital data for the rest of the droid body to know what's going on.
(a bit like BIOS in any regular pc)
Rooting will give you SU access to all files on the phone, be them hidden, system, etc or regular. And then you can move, copy, delete, change permissions etc for any file.
Being that you have SU you can also do more stuff like;
Flash a new more efficient kernel to improve hardware drivers/hardware speeds etc
Flash a new ROM like CynogenMod that you've seen about. This would be the rest of the droid body, and like a droid over a human, it will have various enhancements and mods.
CynogenMod is basically a version of Android like ics or jb but devs have added new & updated features. For instance on your pull down menu (notifications) you might have airplane mode, but on CynogenMod you can change ALL them buttons to be what ever buttons that version of CynogenMod support. So you could change the number of buttons you have there too.
I must admit, I don't know much about bootloader but I'm sure Trent can step in
I'm going to read this post about 3 more times, after my nap and dinner of course... And I will get back to this.
Actually the funny thing is, My VZW rep is completely rooted and flashing crap everyday. He says the same thing, that I should be good, but.... I need a backup plan... in case I screw it all up. As, they say~ a little knowledge is a dangerous thing.... and with all due respect, that's where I am scared.... I only have a little knowledge.
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