[Tests] clearer comparison of HDF5 files

Working on !931 (merged), I found the comparison of HDF5 files against reference files was not very clear. This aims to show all the differences found, not only the first one (i.e. not asserting on each separate step), to present the results in a clearer format, and to simplify the code doing the comparisons.

Based off the branch in !931 (merged), because I know that fails the relevant tests, so I can see what the results look like.

cc @ahmedk