The crux of syncing with iTunes: Data minimization & changing settings

Hello everybody,
I have a couple of questions regarding the syncing of "stuff" between my Mac and my iPhone.
I used to own an iPod (3rd generation, quite a while ago), and I always had my own system of storing music. The thing is, I have my music on CDs: I understand that, in order to get them on an iPod/iPhone, I need to convert them to a different format. So OK, I rip my music and move it to my device -- but why would I want to keep a copy on my computer? I already have two (CD & iPod), why would I need a third?
It doesn't seem to be exactly what iTunes is about, but I did manage (at the time with my iPod and now with my iPhone) to make it understand that I wanted it so. I rip my CDs, move them to my device, and then delete them from my computer.
Of course, nowadays there's the iTunes Store. Since I don't have a physical media for music bought on it, it's OK for that (and only that) music to be stored on the computer -- it's my second copy in case something happens.
When I got my iPhone, it took me a couple of tries to set iTunes up like I wanted to; during those tries, I erroneously deleted and had to re-transfer my music to the iPhone. The "Sync Music" checkbox is, apparently, extremely powerful.
A couple of months later, I find myself in a similar pickle over the apps. With the apps, I believe it to be even more understandable: Unlike with the music, I can't even use the apps on my computer -- so why would I want them there? Some apps, particularly games, have an enormous (storage) footprint! I could save many a gigabyte by not having an (unnecessary) copy on my computer. I have them on my device, and the Store knows which ones I purchased -- couldn't I simply re-download them should the need ever arise (i.e., unrecoverable hardware failure)?
Like with "CD & device" for music, I'd have "AppStore & device" for apps. Everything's backed up. And my hard disk wouldn't be so stuffed.
My iPhone is my primary device for the apps, since it's the only way for me to use them after all. So I download, update, and occasionally delete apps -- all through my iPhone.
The thing is, when I connect and sync it with iTunes, things go "wrong". Apps previously synced and later deleted (on the phone) remain on my computer. I never needed them there, now I don't even use them anymore -- and still there's a copy occupying space on my computer. Worse, those apps want to be updated. Apps that I don't have thus don't use want to be updated. How silly is that? The term "Sync" for iTunes appears to be a one-way process: from iTunes to the iPhone. (At least for most intents and purposes; contacts and calendars seem to work just fine in both directions.) But why? I buy all my apps and all my music on the iPhone. Once connected, iTunes warns me that there is "bought content" on my phone, which isn't on my computer (and it's not as trivial as it should be to transfer it back); but it doesn't know what has been removed.
As I mentioned earlier, the unchecking of the "Sync Music" checkbox solved (most) of my iTunes troubles regarding music.
But I had no idea I'd have to go to the same trouble for apps. (I believe it has to do with the fact that it seemed so absurd needing/wanting to have a copy of an app on the computer where you can't even use it.)
So now I came to realize I probably (I'm not even sure myself) want to do the same thing with the apps as with my music: uncheck the "Sync Apps" checkbox for my iPhone.
But would I have the opportunity to re-download my apps, as I speculated above, should I ever need to? (In other words: Does the AppStore work as a "backup"?)
And, more to the point: How do I uncheck "Sync Apps" without having my iPhone "wiped"?
Toying around with that checkbox is what caused me to have to re-transfer my music to the phone a couple of times. And in fact iTunes states, when I try to uncheck the "Sync Apps" checkbox: "All existing apps and their data on the iPhone will be removed." I don't want that at all!
What is right now: My computer is an incremental storage pool of what was and is on my iPhone, in order to change that setting, the iPhone needs to be wiped of all and any apps.
What I want: My iPhone is my primary app source, I don't want any app on my computer.
What I could live with: My iPhone is my primary app source, I want my computer to be a mirror image of my iPhone.
Ultimately, I have my own system for music and don't need backed up apps on my computer. I use iTunes merely as a tool to transfer data between computer and phone (primarily), as a phone-settings backup system (secondarily), and to manage my iTunes account (really seldom).
I don't need iTunes for anything else. I have my "music machine" (to which I regularly connect my phone, since it contains a lot of music) somewhere else; surely my laptop with iTunes on it isn't the better option.
Does anybody have an answer for one of my many questions? Do you have any ideas or suggestions for me on how to deal with the (quite intrusive and obnoxious) iTunes? They would be greatly appreciated.
Kind regards,
Nicola

Go to here: http://www.apple.com/support/ipodtouch/service/ and read the section called "Connecting to the iTunes store".

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