How comes the portable and regular version are binary identical?
That's because the way Rufus detects whether it should run in portable or regular mode is by checking the file name of the executable. The way it works is like this: if the file name contains the letter p, then the code will run in portable mode. And if there is no p, then regular mode is used. As a matter of fact, on the web server, the download for the portable version is just a symbolic link to the regular version, with a p added to the name, so of course the binaries will always be identical.
But there's nothing fancy or mysterious about this method - software like Busybox has been doing this for years and you shouldn't freak out, or tell me that there an issue with the downloads, on account that the size and content of the portable and regular version of Rufus are exactly the same. There exists many ways to make the exact same executable behave in a completely different manners, through external factors, such as its file name...
De Perguntas frequentes de Rufus
A única diferença que o FAQ menciona está abaixo:
Rufus connects to the internet, but I never allowed it to - why?
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How could I solve this dilemma then? Simple: If you look at http://rufus.akeo.ie/downloads/ you'll see there are actually 2 versions of the latest Rufus version, one called rufus-#.#.exe (as well as the corresponding the portable version) and the other called rufus.exe. They are essentially the same binary file (rufus.exe is actually just a symbolic link to the first one on the web server). However, when Rufus starts, it checks for the name of its executable, and if it finds that it is called "rufus.exe", it does not display the question on whether a user wants to check for update, and enables that check automatically.