If I understand this correctly. The correct way of deploying an MSI bundle
is the following:
1 prepare MSI with MST or any transformation as needed on disk folder
(include any .INI customizations needed)
2 upload MSI including directory structure and files to repository
3 create bundle from uploaded and processed respoitory upload
4 delete disk folder where files were edited (optional but with management
problems, read ahead)
5 deploy and assign bundle to users and objects.

Say I have to update the package with a new transform, how do I re-pull
the uploaded content from the repository back to disk so that I can
re-edit the files on any regular folder or share?

Or should I never delete the disk folder were I edited the files..
The reason I ask is because network install MSI keeps failing... (Message
MSI is not valid, contact application vendor). But when I upload it to the
repository it is valid. When I execute it manually through msiexec /i
"package" it deploys succesfully from the share using runas credentials in
the windows domain.

The whole upload to repository (can't find a way to edit the files and
directory structure, once in the repository kinda beats the whole issue of
storage management. Network MSI folder share is roughly 100 GB, keeping
that in production and als uploading to the ZW10 repository adds another
100 GB.

Why was this design chosen in ZW10?
And why is Network Install MSI failing?