Bloom filters have false positives that can lead to difficult to predict behavior.
The core proble(s) being reported with file dependencies is the size of the download, the
cost of the load, and the size/number of copies one for each location managed by dnf.
These are all problems that are straight forward to mitigate without forbidding file
dependencies.
(aside)
I personally like Bloom filters, and have used them successfully multiple places in rpm
code.