a) Removing "unnecessary zeroes" is not a meaningful optimization. This is not where the processing time is spent when opening a file. Also, filesize is essentially irrelevant. This is an aesthetic consideration(*) and nothing more.
b) The default extension for an MPD file is .ldr. (It is also acceptible to use .mpd or .dat, but in my opinion, you shouldn't.)
http://www.ldraw.org/article/218.html
(*) Bricksmith has an internal option to output formatted columns for easier reading, which is what you're seeing in Ben's file. It's off by default because LDrawers seem to hate it, so I don't know how he managed to obtain it.
b) The default extension for an MPD file is .ldr. (It is also acceptible to use .mpd or .dat, but in my opinion, you shouldn't.)
http://www.ldraw.org/article/218.html
(*) Bricksmith has an internal option to output formatted columns for easier reading, which is what you're seeing in Ben's file. It's off by default because LDrawers seem to hate it, so I don't know how he managed to obtain it.