Yep, unless you change something in the file structure layout, or some other major change, during your manual install, the end result is much the same either way.
Any "hack/mods" that you do are likely to require special attention during at install and/or upgrade time no matter how you install the thing. Obviously, a "once-click" won't include any such stuff, while some "packages" you might come across may.
A "one-click" upgrade of a "once-click" install will overwrite such changes just as a careless manually back up will (though the "one-click" upgrade does "automagically" create a back-up of your old installation (which you should, of course, be doing when you "manually" back up also).
I think it's all just a matter of personal preference. You can have the "one-click" robot install for you, or you can install yourself - the result is the same and each method has advantages and disadvantages, at installation time and again at upgrade time.