Different groups (Ashkenazim, Sefaradim, Teimonim) have different traditions for spellings of different words in the Torah. Practically, while each group writes according to their own mesorah, we consider any of the traditions valid and can use any of them, even for Parshas Zachor.
What about days where the required number of aliyos are read from different Sifrei Torah, like Ch"m Pesach or Rosh Chodesh Chanukah? Can you read e.g. the first three aliyos from an Ashkenazi Torah and the last one from a Sefaradi Torah? Or is this a contradiction, since you're definitely not reading the required number of aliyos from a correct Sefer Torah?
What about Shabbos Rosh Chodesh Chanuka, Shekalim, or Hachodesh, where you have exactly one Ashkenazi, one Sefaradi, and one Teimoni Sefer Torah? Is it required or preferable to add aliyos so that you read 7 from the same Sefer Torah, or does it not matter? (Or Simchas Torah, but then you're probably adding aliyos anyway.)