GerbV version 2.61 (the latest stable) does not support correctly oval drill, so if you merge PTH and NPTH drill files with that tool, you will have a wrong result and you will produce a bad board… and I wouldn’t trust the buggy GerbV beta version (which is not been updated since an year)
I know that kicad is acting in the right way, but at the same time I would appreciate the option to merge the files internally, only when needed to give those files to the ‘blamed’ fabs 