Is there any way for me to change the way that Adobe Muse exports a website in HTML? For example: when exporting a website designed in Muse, the webpages themselves are exported in .html format, while folders for "images", "scripts", and "css" are created for these webpages to source their assets from. Is it possible to have Muse just place the images, scripts, css, etc. folders into one folder called assets so things can be a little bit cleaner for downstream editing? And yes, I know Muse is not meant for downstream editing, which is just another roadblock that restricts it from serving as a professional tool much like Photoshop or Illustrator.
But yes: is there any way for me to change the way that Adobe Muse exports a website in HTML?
Yes, you can do this is your hosting server has all the sufficient permissions and capability of reading the files from any source.
However, this cannot be supported withing Muse, you will have to take help of any third party FTP client like Filezilla or CuteFTP.