Tony Morgan: Bounty Contracts during Setup
Yes, you should be able to place bounties on enemies during setup

Setup instructions from Rules Reference, p.27 (Leaving out some unrelevant parts):


  
  
  Choose investigators. Each player chooses a different investigator,    and places that investigator’s card in his or her
  play area.  
  
  2-3. [...]
  
  Assemble and shuffle the investigator decks. 
  
  5-6. [...]
  
  Collect starting resources. Each investigator gains
  5 resources from the token pool.
  
  
  Draw opening hands. Each player draws 5 cards. Each player, in player order, may mulligan once at this time.  =Each weakness card
  drawn during this step is ignored, set aside (without resolving it),
  and replaced by drawing another card from the  deck. Upon completion
  of this step, shuffle each of these weakness  cards back into its
  owner’s deck.
  
  
  Read the scenario introduction in the campaign guide.
  
  
  Perform the scenario setup instructions indicated by the campaign guide. This includes gathering the encounter sets listed in
  the setup  instructions in the campaign guide, placing locations,
  placing  investigator mini cards at the location each investigator
  begins play  at, setting aside any listed cards, and shuffling
  remaining encounter  cards together to form the encounter deck.
  
  11-13. [...]
  


Now, rules for Permanent cards (RR p.16):


  Permanent is a deckbuilding keyword ability.
  
  
  A card with the permanent keyword does not count towards your deck size.   
  A card with the permanent keyword still counts as being    part of your deck and must therefore adhere to all other deckbuilding
  restrictions.   
  A card with the permanent keyword starts each game    in play and is not shuffled into your investigator deck during setup.
  A card with the permanent keyword cannot be discarded by any means.
  


And let's look at Stick to the Plan


  Permanent. Exceptional. 
  
  Before you draw your opening hand: Search
  your deck for up to 3 different Tactic and/or Supply events, and
  attach them to Stick to the Plan. Shuffle your deck....[Continues]


and Indebted


  Permanent.
  
  You start each game with 2 fewer resources.


This implies that SttP and Indebted must be in play by 8th and 7th step of setup (since permanents are considered part of the deck, I believe they actually come into play during step 4); scenario setup happens during step 10, Bounty Contracts is a Permanent and already in play by then.