I may be missing some issues that I do not understand, but I think there will be no problems doing most of the things you want.

1) Every entry into OCD gets a reference number, no matter how many tracks.

2) You can add all the formats you want to the format list (and delete those you don't need) via View -> Preferences -> Database, highlight Format and click Edit selected list

3) Vinyl sides can be entered as follows. Enter all the tracks. Go to the Tracks tab on the album properties form. Under More is a selection called Start vinyl side that allows you to create A & B sides

I think the main issue with singles is that they don't have a title as an album does. Maybe some others have a solution to this (AFAIK OCD requires something in the Title field).

OCD accesses the Discogs database which might help with some things not on Amazon.