Reading the docs, snapshotting/versioning doesn't strike me as a major feature of perkeep. It's more important and appropriate in the domain of backup software (e.g. restic/attic/borg) and where you'd want it together with delete functionality to reclaim space.
But perkeep's focus, as I understand it, is more on managing an unstructured collection of immutable things (e.g. photo archive), rather than being a tool to back up your mutable filesystem. So I'm not sure they made a good design decision to chunk the sh*t out of my files, which really kills the performance on large files and especially on spinning disks.
Ingest times correlate linearly with file sizes because it needs to compute the blobref (which is a configurable hash) for all the blobs (chunks as you call them). Splitting in blobs/chunks is necessary because a stated goal of the project is to have snapshots by default when modifications are done. Doing snapshots/versioning without chunking would be very inefficient.