When you are designing you use the dimensions that make sense for designing. So if the important dimension is from the centerline then measure from the centerline.
However, it is generally better if you measure something you can easily verify. So in many cases you wouldn't measure to the centerline but rather to the mirror entity, a bit like prefering to measure diameter rather than radius. This has some consequences for the design though, which may or may not be what you need.*
Be aware that your design may need to be flipped which may cause some tolerance issues. Or did you plan for the manufacturer to countersink manually? Also hard corner inner holes are a bit hard to make with the mill, so round the corners.
* So measuring half the distance may in some cases double up distances your general tolerance. But that may or may not come to play check your relevant standard. Remember your document is also your acceptance criteria in cases where something goes wrong.