There appears to be a pattern of non-deterministic cooks when packaging with multiple chunks. In the case of these reproducible steps, only the assets of chunk1 have been modified. In this case, we expect that no changes will occur in chunk2, but changes will occur in .ucas/.utoc of chunk2. This is because the result is different when IOStore is enabled and when it is disabled.
When IOStore is disabled, the .pak of chunk2 is not changed (Diff-DisableIoStore.png). On the other hand, when IOStore is enabled, the chunk2 container is modified (Diff-EnableIoStore.png). Comparing the .utoc diff of chunk2, there is a difference in the hash value of the first content (Diff-pakchunk2.png).
No diffs in pakchunk2-WindowsNoEditor.pak/.ucas/.utoc
Diffs in pakchunk2-WindowsNoEditor.ucas/.utoc
There's no existing public thread on this issue, so head over to AnswerHub just mention UE-135588 in the post.