Unfortunately, it's not hard to find places in the Torah, and even more so in Nach, where we have a doubt about either the trop or the nekudot. (Or, more rarely, letters, but those are generally the sofer's problem and not the baal korei's.) The Tikkun Simanim often notes these on the side.
How should a baal korei, or anyone doing shnayim mikra or just learning, decide which version to use? If you come from a long line of baalei kriah and have specific family traditions, that's great for you, but I suspect most non-Teimonim aren't in that position.
I'm specifically concerned because of this particular example, where the doubt causes a change in meaning. If you don't use the correct halachic procedure for dealing with doubts, and you get it wrong, it's conceivable that you would not be yotzei.