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I don't use qar
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I think .qar files are intended primarily for giving someone else (like a support person at Altera) your design, not for users to create project archives for their own use.
The project archive function modifies your directory structure for any directories that were not originally subdirectories of the project main directory. It moves those directories under the project directory.
Because the project archive function changes the directory structure, it adds user library directories to make it more likely Quartus compilation will find all the needed files in case the archive function didn't update all the pathnames correctly inside the .qsf. (At least I think that's why project archive creates all those superfluous user libraries that annoy me.)
Project archive with default settings doesn't automatically find all files needed for all designs. For example, the user has to tell it to include memory-interface MegaCore .tcl files sourced by .sdc files unless the user has listed these .tcl files inside the .qsf with Project --> Add/Remove Files in Project. To use project archive to capture everything you would want to keep, you would need to go through some of the same exercise Jonas Lindén is doing to decide what files to keep with a version control/configuration management tool.
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