Wednesday's friendly international against the Old Enemy at Wembley celebrates 150 years of the Football Association, with Hodgson using the showpiece occasion to check on the fitness and form of his players ahead of England's four remaining World Cup qualifying matches in September and October.
Rooney is currently struggling with shoulder and hamstring injuries but could still be involved in Sunday's Community Shield match against Wigan - also at Wembley.
And Hodgson admits he will tread carefully with the England forward's fitnesss when he reports for international duty early next week, ahead of the game against the Scots.
Hodgson told Sky Sports News: "My selection of him could be used as a wedge between David Moyes and myself and there won't be any wedges put between us two.
"We've been friends for a long time. David understands my situation fully and put simply we have four very important games coming up.
"I haven't seen the players since we left Brazil three months ago and it's important for me to have them around.
"And even if they can't play full parts in the game - or any part at all - I want them there for these two or three days because we are a squad, we are a team, we are a group.
"Just because someone at this time is not fully fit to play, it doesn't mean they are not going to be an important cog in the wheel come September.
"David and Wayne understand the situation. We'll make a decision. When Wayne comes we'll assess his physical fitness
"And I know David won't mind him taking part in the game but we don't want to put Wayne on the field of play if he is not ready to play.
"The last thing I would want to do is send him back to his club injured and that goes for the rest of the players too."
Rooney has been the subject of plenty of transfer speculation as well, with Chelsea consistently linked with a move for him despite United's insistence that he is not for sale.
Rooney has expressed his excitement at the game against Scotland and took to his official Facebook page, saying: "Can't wait to join up with the England squad and hopefully play in a competitive match - they always are against Scotland.
"Big thanks to Roy Hodgson for selecting me and showing his faith and support - appreciate it."