The Kitzur Shulchan Aruch in 169:1 - סימן קסט - אסור כתבת קעקע says:
וּמִכָּל מָקוֹם מֻתָּר לִתֵּן אֵפֶר וּשְׁאָר דְּבָרִים עַל הַמָּכָּה לִרְפוּאָה, אַף עַל פִּי שֶׁיִֹשָּׁאֵר הָרשֶׁם, כִּי גַם מִמַּכָּתוֹ יִשָּׁאֵר רשֶׁם הַמּוֹכִיחַ עָלָיו, שֶׁלֹּא עָשָׂה מִשּׁוּם כְּתֹבֶת קַעְקַע.
Nevertheless, it is permitted to put ashes and other things on a wound for medical purposes, even if a mark will remain; for (in such cases) the wound will also leave a mark, and it will be apparent that you did not do it for the purpose of tattooing.
So it seems permitted to routinely dig into one's own skin out of habit to the point where one scars their skin permanently.
Also in 91:12 - סימן צא - דין מי שיש לו מחוש וחולה שאין בו סכנה regarding Shabbat the Kitzur Shulchan Aruch says:
סעיף יב'
הַפּוֹתֵחַ מֻרְסָא כְּדֵי לְהַרְחִיב פִּי הַמַּכָּה, כְּדֶרֶךְ שֶׁהָרוֹפְאִים עוֹשִׂים, שֶׁהֵם מִתְכַּוְנִים לִרְפוּאָה לְהַרְחִיב פִּי הַמַּכָּה, הֲרֵי זֶה חַיָּב, שֶׁזּוֹ הִיא מְלֶאכֶת הָרוֹפֵא. וְאִם פְּתָחָהּ רַק כְּדֵי לְהוֹצִיא מִמֶּנָּהּ אֶת הַלֵּחָה שֶׁמְצַעַרְתּוֹ, וְאֵינוֹ חוֹשֵׁשׁ אִם תַּחֲזוֹר וְתִסָּתֵם מִיָּד, הֲרֵי זֶה מֻתָּר מִשּׁוּם צַעְרוֹ. וְדַוְקָא לְנָקְּבָהּ עַל יְדֵי מַחַט וְכַדּוֹמֶה אֲבָל לֹא בְצִפָּרְנָיו, מִשׁוּם דְּתוֹלֵשׁ קְצָת מֵעוֹר הַמֻּרְסָא, וְיֵש בָּזֶה חִיוּב. וְגַם עַל יְדֵי מַחַט וְכַדּוֹמֶה, כֵּיוָן שֶׁיֵּשׁ לָחוּשׁ, שֶׁמָּא יִתְכַּוֵּן שֶׁתִּשָׁאֵר פְּתוּחָה, כְּדֵי שֶׁתּוֹצִיא לֵחָה גַּם אַחַר כָּךְ עַל כֵּן אִם אֶפְשָׁר יֵשׁ לַעֲשׂוֹת עַל יְדֵי נָכְרִי.
One who punctures an abscess in order to enlarge the opening of the wound, in the manner of physicians when they attempt to facilitate healing by enlarging the opening of the wound, is guilty of a Shabbos violation, for this requires a doctor's skill. If his [purpose in] opening it the abscess is only to drain the pus, which is causing him pain, and he is unconcerned if the [opening] closes up again immediately, this is permitted due to his pain. [This is permitted] only when he punctures it with a needle or something similar. But, [he may not do so] with his nails because he then tears some of the skin of the abscess, which makes him liable [for doing a melachah]. Even by means of a needle or something similar, there is concern that he may want the wound to remain open, so that the pus will continue to drain, therefore, wherever possible this should be done by a non-Jew.
Seems that the only concern is Shabbat-related and causing permanent changes to one's body is not an issue.