Konami (and EA) also gets the branding, the likeness to Old Trafford, the kits, the player faces. FM doesn't. From the reports, the club's issue appears to be that they've used the name without the branding as a way of circumventing the need to acquire licensing.
I'm dubious that Football/Championship Manager (and various other manager sims) has been using club names for 30 years in a way that infringes the law, as it surely would have been actioned by now, no? The recent PES deal isn't the first time the club has licensed its IP to video games. There has been loads of United branded video games, particularly in the 90s. Why now?
If United demand that FM don't use the name anymore, it would probably be more damaging to the brand if all 19 PL teams are named correctly except for "Man Red".