Can you share that config? Sounds useful!
I configured all that literally years ago so I don't remember where's what but here's what I've got:
;; probably cargo-culted from somewhere
(update-glyphless-char-display 'glyphless-char-display-control '((format-control . empty-box) (no-font . empty-box)))
;; See https://emacs.stackexchange.com/questions/65108
(set-face-background 'glyphless-char "purple")
And then I've got this too (requires markchars.el): (markchars-global-mode)
With: (defface markchars-heavy
'((t :underline "magenta"))
"Heavy face for `markchars-mode' char marking."
:group 'markchars)
It should get you started.(and, yup, I know it's overkill but I like it that way)