fix tests with --generate-reference flag

[epassaro]

Description

• Use to_hdf method with new overwrite=True when required.
• Removed unnecessary if statement for old pytest versions.

Motivation and Context

Test failed with --generate-reference flag since #1366 was merged.

How Has This Been Tested?

• Testing pipeline
• Other (please describe)

$ pytest tardis --tardis-refdata=/path/to/refdata --generate-reference

Screenshots (if appropriate):

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• None of the above (please describe)

Checklist:

• My code follows the code style of this project
• My change requires a change to the documentation
• I have updated the documentation accordingly
• I have built the documentation on my fork following these instructions
• I have assigned and requested two reviewers for this pull request

[codecov]

Codecov Report

Merging #1399 (7ee2a08) into master (e8ef961) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1399   +/-   ##
=======================================
  Coverage   70.04%   70.04%           
=======================================
  Files          67       67           
  Lines        5312     5312           
=======================================
  Hits         3721     3721           
  Misses       1591     1591           

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