edge connector is off-the-shelve, but I only have a China number, which would reveal my source. Please understand that I won't publish that. You'll surely find an IDC edge card connector at the more specialized sources (tried digikey, but either they don't have it, or their search/filter function is cr*p).
The polarity notch is a custom laser-cut piece of metal inserted in that connector. All these connectors have positions inside of them for a polarity-insert, but I haven't found anyone who delivers those inserts, which is the reason for making a custom part. It will work without a polarity insert (naturally!), but then you'd open up the danger of applying unfused +5V to a pin where it doesn't belong.
the additional connector is for future use. I plan to make adapters for less-popular computers like Atari ST, so I have put all 24 colour-bits and a few more CPLD pins on that connector. It's a bottom-entry type, so I have more flexibility in the mechanical design of that no-yet-existing-adapter (that type of female header allows inserting pins from both sides). Using such an adapter will require a different CPLD program, so it will not be an A1200 unit any more.
The unused mountholes account for different mainboard versions. Some of them have SMD components in the way, and in that case, you can re-position the stand-off. Also, every mount hole can be used for additional grounding.