Apps supposedly takes up almost 1TB on Sonoma (not true) - how to fix it?

The issue might be ? that the drive has 2 Macintosh HD - Data Volumes

Use the link below to remove the extra Volume

Add, delete, or erase APFS volumes in Disk Utility on Mac - Apple Support (CA)

FYI, The information in the Storage Management area has been known to be incorrect. I've seen some references that it may be an issue with the Spotlight indexing, but that is only one possibility. Plus storage information when using the new APFS file system can be complex due to new features available with the APFS file system. The most important thing to check is the actual amount of Free storage space. Unfortunately the only places macOS actually lists the Free storage space value is within Disk Utility or within the Apple System Profiler's "Storage" section.

Most other places in macOS will list "Available" storage which is very misleading for people since "Available" storage space consists of both Free space and Purgeable space.

Free space is storage that is able to be used immediately.

Purgeable space is storage that will be usable at some unknown time in the future.

You can easily calculate the actual Free space since macOS usually lists the Purgeable value with the Available space.

Free space = Available - Purgeable

I know this does not help now that you erased everything & reinstalled, but it is something to consider in the future when looking at storage on an APFS volume.

Out of curiosity, what apps are listed when you click on the circle "I" next to applications in that disk storage window? Do the sizes in that window add up?

This is not a flippant reply to this computer issue

Yes, you are probably correct.

The Applications, normally , should not be taking that about of Storage

Though, you may start Trouble Shooting the issue by >>

Any Third Party Applications that will interfere with the normal operation of the OS,  is an invitation for disaster. 

Certain Applications maybe available on the Apple Apps Store - this only means the Developer is prepared to pay Apple a portion on each sale. 

What the Application may do to the computer is up to the User to check this out before purchase

Any of the below should be removed as per Developers Instructions 

1 - Disk Cleaner 

This will include CleanMyMac , aka “ BrickMyMac “

We have supplied a link to search the Apple Support Forums

It is to see the types of Issues this specific Application may have been inflicted on this machine and the severity of the problems it may have caused.

They can range for Borking your Home Folder ( User Account Folder ) resulting is very inaccurate Indexing of Data Reported as Used by Applications

what I do is make sure I only use Unreal or Pure Silicon applications! I also use to use application ONYX and run all of 'Maintenance' tab is selected and run all the cache cleaning/rebuilding routines about once every two-three months to delete old cache files and logs!

Then have a few suggestions ;

1 - Get Support Choose a product and we’ll find you the best solution.Start now and open an Apple Support Ticket as they are PAID  Apple Employees to deal will these types of issues . 

2 - Product Feedback - Apple and make it known to Apple regarding this ongoing issue