This post triggered some memories of an edge connector I made quite some time (2 to 3 years) ago.
I manually had to renumber most of the pads. It was not such a biggie because I only did it once. If you do it more often however, a better approach is to draw a one dimensional array of pads. (One for top, One for bottom).
I was a bit confused of how this worked exactly, and therefore started this thread because I expected a bug (but was not sure).
However, after Rene pointed out the entry boxes I glanced over and used them, it all worked as expected.
Also, when designing new footprints from scratch, I find it helps if you start by making some sketches on good old dead tree carcasses, and then punch in some numbers for important coordinates.
If you have some coordinates, you can simply put those in the X and Y coordinates of a pad instead of lining them up visually.
Or make good use of the grid. Use a grid that is relatively coarse when placing pads in the footprint. If you visually line up footprints on a coarse grid, then either coordinates are perfect, or the mismatch is so big that you can clearly see it.