Yes and no. If you check the size of the packages folder by right clicking on it and choosing properties then it will show something like like 6Mb. But, if you open the folder and check the size of everything inside it then it shows 145Gb on my system. That is if it is a virtual folder. MS Store games like to use these weird virtual folders.
Another way to be sure it’s a virtual folder is that the contents of the Packages folder on the C drive should be a bunch of folders with little arrows in the corner of the folder icon (this shows that they are shortcuts to somewhere else).
If all of the above isn’t true then you likely do have duplicated packages. If that’s the case then try renaming one packages folder and start the game. Does it work? If so then you could likely delete the other folder. Try renaming them before deleting them to see if anything breaks. That way you can figure out which one is really being used. .