Agreed with @codebrainz it's not very clear, but I guess I got it:

When filetypes.php has an empty comment_single, it uses HTML comments (<!-- -->) instead of multi-line PHP comments (/* */) for some reason.
To test:

1. Open Geany with a stock configuration (geany -c /tmp/temp-config)
2. Create a new PHP file from template
3. Insert a non-empty line in the PHP section (e.g. echo "hello!"; on line 24)
   1. Try and comment line 24 with Ctrl+E: it inserts //~ at the start of the line. Good! Try and the same on line 31: it inserts <!-- -->. Good again! Toggle both back to not commented.
4. Open filetypes.php (Tools → Configuration files → Filetype configuration files → Scripting languages → filetypes.php)
5. Change the value of comment_single to make it empty. Save it.
6. Try commenting line 24: it inserts <!-- --> 😞

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