According to the manual, for the 2.4L, you have the following dimensional ranges for stock pistons and cylinders:
Piston OD - 3.4434" to 3.4441"
Cylinder Bore - 3.4446" to 3.4452"
That puts line-on-line clearance between .0005" and .0018"
That means, if you're using a +.50mm piston, keeping the same clearance, those numbers become:
Piston OD - 3.4631" to 3.4638"
Cylinder Bore - 3.4643" to 3.4649"
But you're measuring bores to be 3.4513" to 3.4515". If your interpretation of the piston markings is correct (and it does make sense to me), and you are correctly using your bore gauge, your bores are about 12 thou smaller than your pistons. That's not possible (assuming these pistons were in the cylinders at one time). Measure your pistons. If they are between 3.4631" and 3.4638", your interpretation of the markings is definitely correct, and the logical conclusion is that you are not getting correct bore readings from your gauge, either from improper use, or from a broken bore gauge. That's where my money is.