Can Black always choose seating position and clock position? Watching tournament and competitive club play, players playing black sometimes switch the clock to their dominant side before the game starts without asking. 

Presumably, having the clock on your dominant side compensates slightly for losing the first-move advantage because it makes it easier to operate the clock for you, it makes it harder for your opponent if they have the same dominant side as you, and it may serve as a small psychological crutch — particularly during blitz games.

But FIDE’s Laws of Chess state that:


  6.4
  Before the start of the game the arbiter decides where the chess clock is placed.


Additionally, I’ve seen Black switching the board around before either player has sat down so that they get the view of the room they prefer. IM Jeremy Silman even gives this tip in his “Psychology” section of The Complete Book of Chess Strategy:


  If you’re playing outdoors, don’t forget to face your opponent towards the sun (it worked five hundred years ago and it will still work today)!


Which must be a reference to this quip:


  Sit your opponent with the sun in his eyes.
  — Ruy Lopez, 1561


Two questions:


As black, will I get in trouble for moving the clock before the game without asking?
As black, is it an acceptable practise to ask to trade seats?


Answers can refer to casual play, club play, and tournament play.
It is an interesting question, but you already gave the answer. It is the arbiters decision where the players sit and the clocks are placed (so that the arbiter can see them best). When no official arbiter is present, the team captain of the home team acts as arbiter. These rules are for tournaments and club matches. Casual is of course different.
If a player does not follow the arbiters decision he can get penalized (eg. time reduction, which happened few months ago at our club match, because of the exact same clock positioning question)