I am trying to create an automatic \"sitemap.xml\", I already followed the instructions provided by Google to create one, and here is what I currently have:
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The answer to your question is: yes, you can embedded PHP in XML. PHP is specifically designed to be embedded: that's why tags exist in the first place. And PHP doesn't know or care where you embed it as long as:
Such answer is basically irrelevant given what you want to do. Google sitemaps are XML files with a very specific syntax. Injecting the HTML code of your main menu will not make a sitemap out of it, just like opening a MP3 file in your text editor and typing your name in the middle of it will not make Freddy Mercury sing it.