I have heard that a haftorah klaf (scroll) is still considered kosher and usable if the Ta'amei Mikra have been written on it. Yet I've always been told that this is not true for a Torah scroll. Why the difference?
Wow, I was fascinated by the question, so I looked it up...
First, an introduction of a central concept: There is a disagreement that wends through the Talmud (like Sanhedrin 4a,b) regarding the words of a Torah scroll whether "Yesh Aim leMikrah" or "Yesh Aim leMesoret". Roughly translated, that means "Primacy is given to how it is read" or "Primacy is given to the Tradition". So, for example, the Torah says not to cook a kid BCHLV IMO. Without a Tradition, you might read that as BeCHeLeV IMO, in its mother's fats. The Tradition tells us to read it BaCHaLeV IMO, in its mother's milk. Should we give more legitimacy to the first interpretation unless we have a special indication that only the Tradition applies? Or should we work with the Traditional reading unless there is a special reason to consider the simple reading as well?
Now, to begin the answer... The prohibition of using a Sefer Menukad (vowelized scroll) in Shulchan Aruch is in YD 274:7, and in the Ta"z 6 & 7. For simplicity though, I'm translating Keset HaSofer 16:6: "A vowelized Torah Scroll is pasul because we have established that 'Primacy is given to the Tradition', and once it's vowelized there is only 'how it is read' [which is to be secondary]. And even if they should remove the vowelization, it remains pasul! Since the intention of the scribe was that he was unconcerned about the Tradition but only to 'how it is read', and for this purpose he wrote it, it is as if the document condemns itself as a forgery ("Mezuyaf miTocho"). [Ta"z] But had the Torah Scroll already been written properly, and then they added vowels or cantillations, scratching out would help as it does by other errors..."
The rules for writing Megillot are in OC 691. Law 9 simply reads, "A Megillah that is vowelized, and similarly if on the first page are written the blessings and poems, is not disqualified thereby." No explanation is given to the difference, as if it were self-explanatory.
Presumably, the difference is the Torah Scroll's requirement to conform 100% to the Mesoret, the Tradition from Moshe at Sinai through Ezra, whereas the primary requirement of the Megillah is to be read properly, and if the vowels help, so be it...