Not an expert, just like Amaryllis and growing them.
1. I had this happen to my newest Amaryllis this past year, the bulbs had been in the pot for approx 7months and all 3 bulbs had put up normal sized stalks and flowers, I noticed after all of the blooming had ceased that one of the bulbs put up a flower on an extremely short stalk like yours. I have never seen one do that but I've only been growing them for 13 plus years...I just chalked it up to a bonus flower at the end of the growing season.
2. Your mix sounds fine, I usually just use a potting mix plus some compost.
3. Don't believe not separating the bulbs produced an adverse effect, Amaryllis like to be pot bound, I usually do not repot the bulbs unless than I have less than an inch between the bulbs and the pot.
There are other Amaryllis devotees on this site and can add information.
