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I'm in a similar boat with the OP. I maintain my files in a PhpStorm Project. This allows me to use Git to maintain version control with a remote repository.
If I'm understanding things, Open With would allow me to edit an individual file in PhpStorm, but would not allow me to deal with them *inside* a PhpStorm project. It would also launch PhpStorm each time I wanted to edit a file, which would be quite slow.
Having them in a PhpStorm project allows me to set project-specific coding standards and inspections as well a live templates and many other features not available in the Sigil editor, such as custom autocomplete and instant error checking and correction. PhpStorm can do this only because it's aware of all the other files in the project.
Inside the project, I can also use SCSS for the CSS code and have it auto saved to a .CSS file when saved.
My not-so-brilliant idea was to extract the files from the Sigil ePub with 7zip, work on them in PhpStorm, then either rezip them to .ePub or delete all files in Sigil and re-import them. As you've made clear neither of these is likely to work (for one thing, re-importing them trashes some of the external links in a book).
An "Import and truly replace" files feature would be a Godsend for me, though I can see why it might not be worth your effort.
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