(The original question asked if there are any, but there aren't, hence the update).
The famous ו דגחון Sugiah in Kiddushin 30a:
"א"ל: ניתי ס"ת ואימנינהו, מי לא אמר רבה בר בר חנה לא זזו משם עד שהביאו ספר תורה ומנאום? א"ל: אינהו בקיאי בחסירות ויתרות, אנן לא בקיאינן"
Said the scholars to him, Let a Scroll of the Torah be brought and we will count the letters! Did not Rabbah b. Bar Hanah say They did not stir from there until a Scroll of the Torah was brought and they counted them? [and the letters did not match, so they said] — They [the Sofrim] were thoroughly versed in the defective and full readings but we are not.
Clearly, the Sefer Torah they possessed was different from one of the Sofrim (some 400 years earlier), and they attributed the difference to יתרות וחסרות (writing Hebrew words in short or in full) in other words to actually altering the letters of the Torah scroll in some way. But this fact didn't surprise the Sages, they attributed it openly to their insufficient knowledge of spelling the Hebrew words according to the tradition.
It seems, that the divine Torah given by Hashem could easily contain means of foolproofing/anti-altering codes, for example, start every line with the same letter line, have fixed skip-length words for the whole Torah (like ת-ו-ר-ה every 50 letters) and more.
Considering the importance of every letter in the Torah and the most stringent Halachah about invalidity of a scroll that lacks a letter, I would expect the Torah to include those marks (which would also make it very different from a regular book).
Why, after all, those measures are absent in the Written Torah?