You can remove the existing web.config file that is in the zip.
Just a quick question for you Mitchell. Does it make any difference if one just modifies the existing web.config? I did that on a clean install for testing 4.5.1 and it installed beautifully. Took about 15 minutes, including setting up the new DB, virtual directory in IIS and setting Asp.Net User permissions.
I was very "wary" about 4.5.1 having seen so many negative posts, but so far I am pretty/amazingly happy with what I see, especially all the work Locopon did on FCK. I tested loooooots of editors, FCK, FTB, Free Text Box, TinyMCE, etc. a while back and FCK was way beyond the rest. Good work Locopon!!
In any event, unless there is something I am missing, shouldn't modifying the existing web.config in either a fresh install, or an upgrade work just fine?
Clay