The black thing on the tall pipe is your spa air blower. It could be lower, just as long as it's not so low it starts sucking debris from ground level.
My spa does fine without a blower; with pump speed over 3000 rpm, it sucks enough air without needing a blower. Perhaps you could do away with yours if it bothers you. If you do so, get a 180° PVC bend so the intake is pointing down.
As far as skimmer lids, I dunno. That one looks pretty standard. It seems more dependent on the height of the skimmer itself relative to the deck. You might try taking a lid to a pool store and see if they have something the same size but flatter.