If you're replacing the rear speaker then, of course this is not optional. If you're following these instructions in order to replace some other component (the MagSafe connector seems to be one example), then it probably is optional. FWIW I repaired a damaged speaker by applying some flexible rubbery glue with a toothpick to the cone surround to seal the hole. It doesn't look pretty but it sounds fine.

The SODIMMs don't need to be low voltage DDR3L (i.e. 1.35 volt). In fact Apple recommends (https://support.apple.com/en-gb/HT202593) regular 1.5 volt DDR3 and most late 2012 Mac Minis were shipped with it. So is Crucial wrong? The truth is that either will work.

Answering my own question, the clips re-engage when the lower case is correctly positioned. You can help them by gently pressing the lower case with your thumbs midway along the two short sides. When everything is correctly aligned the eight screw holes line up.

Yes. You can replace it with another optical drive, replace it with an adapter containing a hard disk or leave the space empty if you wish. Obviously you would lose functionality but you would save a little weight.

Do the retaining clips have to be re-engaged when replacing the lower case?

Note that it has to be 1.5 volt DDR3 RAM, not 1.35 volt DDR3L.