The following code will also fix the case of # as delimiter for s///.

Example: typing s#a#b##comment leads to

s#a#b#                         # comment
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V0.04

(defun my-indent-for-comment (arg)
  "DWIM indent-for-comment v0.04"
  (interactive "p")
  (cperl-update-syntaxification (point) (point))
  (if (and
       (not (memq (preceding-char)  '(?$) ))
       ;; (memq (preceding-char)  '( ?\; ?{ ?\( ?\[ ) )
       (memq  (get-text-property (point) 'face)
          '(cperl-my-trailing-spaces-face nil))
       (not (get-text-property (point) 'syntax-type))
       (looking-at "[[:space:]]*$")
       )
      (cperl-indent-for-comment)
    (insert "#"))
  )
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checking the "face" may be redundant now...