Would it be technically mutar to make any kind of note on the klaf of a sefer torah? (For instance, marking where the aliyah ends) If not, what would the issue be?
We should not be adding anything to the sefer torah. The reason is because the sefer torah has to be the same way that we got it from Moshe Rabbeinu. The same applies to a mezuzah. not to add anything to mezuzah
Y:D 274-7, Taz ibid 7, not to make markings to separate the pesukim or to make nikudos (vowels) in the sefer torah. Rema 288, See Rema O:CH 691-2 regarding a megillah.