You can get really close with drill extensions that allow you to drill from the hole positions in the back to the seat. If you do have sufficiently stiff spindles, or one so flexible an offset will cause the back to assume a different position, then you can make a template of the holes from the top, and actually center the drill extension exactly with the upper hole while drilling the lower.
Under his earlier name, John Alexander has a very interesting video that details ladderback construction. One of the eye opening things about it is how he rigs his brace-and-bit with extensions to drill with more freedom and the same accuracy as a drill press. Very eye opening.