Could you please help me understand the logic behind certain things in OSX?

Ok, so I try to be an open-minded guy, and I bear no particular allegiance to either OS. I own a Sony TZ and a Mac mini, and my wife has a MacBook Pro. I use both Oses.
There are certain things I have trouble understanding in th Mac OS, so what I'd really like to understand the logic behind certain design decisions in the OS, and why these might be better ways of accomplishing things. I know how to get around all of the things I mention, so I'm not looking for instructions; rather I'm looking for well-thought out explanations for why these features are the way they are.
*1. Programs don't quit when you close the window.*
- This totally puzzles me. Why design it so that program windows are independent are from the running program itself? There must be a reason, cold someone explain how this is more efficient? To me, it's simpler to click an X on the window you are working on to completely shut down a program, rather than to either mouse through menus to select quit, or be obligated to using Command Q keyboard shortcut.
*2. Menu bars are on the desktop.*
- Related to the first point, why make the main thing framing your desktop be something which is always changing depending on the program? Why have file menus outside the main window of the program. Having the menu bar on the desktop then necessitates an additional area, the dock, which has to be used as a launch bar and to tell you what programs are currently running. That obligates you to having 3 different areas of screen: 1 for program menus, 1 for running programs, and the program window itself. This seems very inefficient to me. Not to mention all the messy-looking floating palettes all over the place, again because everything is separated and not nicely contained in a single program window.
- Really, having a changing menu bar that frames the desktop isn't even consistent wth the whole desktop metaphor, which is that you place things on a desktop, like programs, files, etc. Are you changing the whole desk everytime you load a new program, yet the wallpaper stays the same? Doesn't seem to be logically consistent to me.
*3. No delete key.*
- This one really gets me. Why make such a commonly used key be a function key (Fn + Backspace)? Why make the user press a secondary key for a major function?
*4. No Cut command.*
- I read something about how Cut doesn't actually make sense when moving files around, but I obviously didn't fully understand it. Why make the user command drag, when you can just do Ctrl X??.
*5. Launching Apps from the Finder.*
- This seems weird to me, that you find and launch applications from the same thing you use to view files. Program icons in the finder are placeholders for the entire program, not files, yet they are found in the file viewer. Again, to me this seems logically mixed. I really dislike scrolling through Finder to look for apps. I know there is Spotlight and the dock (used as a quicklauncher), but these are really just workarounds for a setup which seems inherently illogical. To me at least, a menu of applications make more sense, ie, the start menu.
Anyway, those are all I can think of now, although there are other things aout OSX that don't make sense to me.
Thanks in advance! If I can understand Apple's reasoning and it is convincingly better, that will go a long way towards making me more comfortable with this OS.

1. Programs don't quit when you close the window.
That's really more a matter of what you're used to. It comes down to a programming decision as to what Apple and Microsoft considered to make sense. MS thinks that if there are no open windows, you're done using the app. Apple thinks you aren't necessarily done yet, as others have mentioned. I certainly wouldn't want Photoshop to quit every time I closed the last open image I was working on. Would be nice though if Safari would quit when I close the last open browser window. It's quick to relaunch if you really weren't done with it, so wouldn't be much of a bother to have it shut down with the last window.
2. Menu bars are on the desktop.
Makes way more sense the Microsoft's approach of repeating the same file menu on every open document in a program. How many places do you need to see File, Options and other common menu headings?
2. Menu bars are on the desktop.
Related to number two. The forward app is the only one you can directly work in, so why not have the menu bar change to reflect the choices for that application? When you go back to the previous app you were in, the menu bar changes back. So what loss of functionality is there? It comes back to not having menu bars on every single open window. There's no need or purpose for it.
3. No delete key.
Backspace does the same thing.
4. No Cut command.
Command+X, not Ctrl+X. This is Mac, not Windows. There's also very little need to ever do this from the keyboard. If you're moving files that are on the same drive/partition, then just drag and drop from the target folder window to the source. It's automatically a move. If going from one physical drive or partition to another, it's automatically a copy. Press and hold the Command key during the drag to make it a move.
Besides, you don't really think Windows cuts the entire folder or file contents into RAM, do you? If your computer has 4 GB of RAM, and you cut 12 GB of data, it of course can't possibly fit in the clipboard. All Windows does when you do a cut is visually remove the files and folders from the screen. If the items are going to a location on the same drive/partition, it does the same thing as if you did a drag and drop move. The file table is simply updated to reflect the new file or folder locations. If it's to a different drive/partition, it then performs a copy then delete action, same as OS X.
5. Launching Apps from the Finder.
A program is just as much a file as any other file. It takes up space on the drive. The OS of course knows what to do with it when you double click an app. Same as it knows what to do when you double click a document related to an app. Windows is no different. An .exe file is also just as much a file as a .doc file. The .exe extension tells Windows to try and treat it as a program to load into RAM. It's not just a simple placeholder. The program has to be made up of something.

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