Mod 42 actually said what I was going to post.
In matters of Torah reading, the nekudos must be accurate, because the entire meaning of a word can change, and the Torah was given directly by Hashem. In matters of davening which are primarily tefilos that were written by people (unless it is something like the Shema, which comes from the Torah), there is a teeny bit more wiggle room for alternate pronunciation of certain vowelizations and all are acceptable.