If I understood correctly what you ask, then no there's nothing like that.
it would require more than a loader to do that, it would require a database and a manager to analyze all your data on your drive, and makes a map of each sectors/clusters of all used files, then provide to cIOS identical position for different launched games. if you delete a game, it has to remember if that position is still shared with another game or not before physically deleting it from your drive, if you use your simple windows file explorer to copy/delete files then you'd corrupt the database.
there are few terms which are approching what you talk about, but it's not that :
-deduplication : using the same physical file location for multiple instances. It's used by Mediafire, when you add a file to your private space it first checks its checksum, if someone else already uploaded that file then it doesn't upload it again, instead it adds it in your file list and links it to their unique copy, it takes 1 second instead of uploading/taking storage space again.
- Sparse file : works like scrubbing, but it's a NTFS feature done transparently to you. It saves hdd space by analyzing the file's data, if there are redundant data (like a big part filled with 0x00), then it stores it only one byte and keep the count of how many it should contain. the file is as big as is should, but takes less physical space on your hdd.
What you want is a mix of both. I don't know if there's a word for that.
analyzing multiple files and "sparse" them to prevent copying some parts of the file and use a single instance of sector or cluster for each shared content.
What could have been done, years ago, is create a program which generates a text+bin files with only the different parts of two compared files, and make the loader loads that text+bin file.
It would have not require a specific database do maintain multiple games or all the hdd, but only a single file compared to another, with the result binary listed as full game in the loader.
the idea is nice, and it would have been possible due to how the wbfs format is working : list of segments, no file system is used by the cIOS.