In practice, the deduplication is pretty good. I have 78 Flatpaks installed (apps and runtimes), and here's my dedup stats (calculated from https://gist.github.com/powpingdone/001a46aa7db190b9c935f71c...):

  ===========================================
  no dedupe: 16.0 GB (17228518418 B)
  dedupe:    11.7 GB (12594871766 B)
  singlelet: 8.1 GB (8677649129 B)
  orphan:    1.8 GB (1889889290 B)

  ===========================================
  deduplicated size ratio: 73.10
  singlelet space usage:   68.90
  singlelet file ratio:    63.56
  orphan space usage:      15.01
  orphan file ratio:       2.63