1. If I'm going to ever be back or play on upselling more work, I'll make my life easier with a panel that has some spaces left in it. If it's strictly $$, I'll tend to go as cheap as possible. But before I leave zero spaces, I'll ask the question if they want to spend a few more bucks to have some extra blanks for the future. Usually they want to go up just a tad to save ripping out a new install to replace it when the whirlpool tub goes on sale at the big box store.
2. Same as #1. If I have to move a breaker from the main panel to the sub, it makes life easier if they're the same ones.
3. Generally I'll try to line up the tops of the tubs. If I'm mounting one below the other, I'll line up the centerlines unless there's a wall of something that make me rather line up one of the sides instead.
Personally, I would have thought: line up the tops of the panels. Then I did a bar / restaurant remodel.
After all the beer signs and mirrors and artwork was hung by the customer, I stepped back and looked at the result. The customer, under the direction of his watchful wife, placed each item exactly where sh directed. The end result? Almost a perfectly straight line along the bottoms of them!
I think that if you visit a few local restaurants, etc., ... you might begin to see a pattern. It sure seems that way to me - things mounted 'above the waist' seem to be lined up with the bottoms even- at least more often than not.
Going by the fact that most of our boards over here will be flush-mount as opposed to surface-mount, you would have the top of the sub-board level with the other board.
Future expansion is something that is an un-written rule amongst Electricians here, you never install a panel that only takes into account, only YOUR circuits. Simply because, you could be the one, down the track that has to add new circuits in the future. Why make life harder for yourself or the next guy just for the sake of a few dollars. This is what Trade Practice is all about.
I have seen it done all different ways. I myself would always leave some extra room. Hopefully, I was the one to go back and do more work on the house. I would ask the homeowner if they were going to do more work on the house, if so then I also would offer several options, like asking the HO if they wanted to upgrade to a larger panel.