How to locally backup multiple iPhones with different IDs

Hi all, I have a simple need to backup 2 iPhones using different Apple IDs. I understand that I can use iCloud to backup each on the cloud and no issue there. But when I ran local backup for both on the same computer, here comes the problem...
The 2 iPhones have some overlapping apps, but separately purchased on two accounts. It seems that iTunes only keeps one copy of those overlapping apps, namely only the copy using the ID of the first phone in the sequence of backup. So when I try to restore on the second phone, it will simply install those overlapping apps using the copy stored locally, which does not belong to the second ID. This seems to create a lot of confusion later on when apps are updated, since the second user will be prompted to enter the password of the first ID.
I suppose this kind of scenario is not uncommon. Is there a way iTunes can properly deal with this? Or did I not do the backup/restore correctly?

Thanks, Lyssa. I guess that probably will work, but feels like an overkill for a simple task.
By the way, I am using iTunes on PC. So the default path for media folder is C:\Users\USERNAME\Music\iTunes\iTunes Media, and the apps are stored in the Mobile Applications sub-folder under that path. I wonder whether it will work to backup the first phone as usual first, change this path in the Advanced Preferences to another user created folder, and then backup the second phone. During restore, I assume one can do the reverse and restore each phone while this path in preference is set accordingly.
That's just an idea I have come to, inspired by your solution of changing user account... haven't tried it out yet. I have to say, even that sounds like an inconvenient workaround. Is there any more elegant method I wonder...?

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