Best practice: male spigot goes into 4" pipe or 4" fitting. Not female, not 3"
Flange height - on top of floor [1]. This is because bottom of toilet is recessed [2]
Thread with clear conclusion that bottom of toilet flange sits on the finished floor. [3].
Here my main man is not so hot - says that flange can be flush with finish floor, not on top of finish floor. [4]
Key insight about flange types - Toilet Flange

Standard Design

Standard best practice is to use 4"x3" closet bends. If it is 3" on top, it is more prone to clog. [5].
Note that the 4" top design is more tricky for the ground floor, where an extension pipe must be used from below the concrete in order for rough-in plumbing to clear the bottom of the foundation rim. Otherwise, you are sending PVC through concrete. Due to this - we use a 4" riser for the first floor toilet. This leaves only the option of using a toilet flange that is '4" inside fit', such as this [6] - meaning it actually fits inside 4" schedule 40 pipe, not into a pipe coupler (closet bend top end) as on the second floor.

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