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 <kbd>Ctrl+E</kbd>: 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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