Some pistons are stepped but they were normally flat when new. Over sized pistons are generally 3 mm shorter to compensate for increased compression due to over boring so stepped pistons only add to compression loss. I'm not a big fan of stepped pistons and will only use them if nothing else is available. In some cases I will deck the block to return proper piston height. Compression is HP on our engines and knowing how far to take machining is key to a strong engine.
I've seen engines where the pistons were .020" under deck height. I've also seen engines where the pistons were above the block parting surface .020" which is allowed. Ideally, you should aim for deck height if possible.