Installing IDE by using "Windows Installer" vs. "Unzipping Zip File"

My appologies if this has been asked and answered already. I did a search, but the search tools aren't very good. I wish you could search only the titles.

I have a Windows-7 64 bit OS. What are the pros and cons of using the "Windows Installer" vs. "unzipping the zip file". Are there any gotchas?

the only gotcha I have seen sofar is that it tosses it in the program files(x86 I think) folder and you go in and edit a file in there, like boards.txt it will fail to save due to permissions

now you can change permissions, or in these newer versions you can have another boards.txt in your sketchbook and it will append (or cores or libraries etc) so its not really that big of a deal