When you select Migration Assistant, it migrates all apps. You cannot pick and choose which apps to migrate. Even if Boot Camp migrates it's not a big deal at all, it takes up little storage and no one says. you have to use it. I have had it installed for years on multiple Macs but have never used it and even forget it's on my system. In other words, don't worry about it, it's really a non-issue.
One thing you can do if you want is when you migrate Migration Assistant asks what you want to migrate. Your choices are:
- Settings (I always migrate these)
- Data (I also migrate all that)
- Apps
So that means if you don't want to migrate your third party apps you don't have to. It means you simply have to manually install them after you have migrated. Personally I don't find that useful and migrate all my apps. But that is just my preference.