fix: fix Structure loading with close-duplicate atom

[stevenhua0320]

@sbillinge ready to review. This is the potential solution proposed by @Tieqiong last summer diffpy/diffpy.pdfgui#291. We change the order of the source that we trust most as the priority. After this is merged and released, we could ask whether this fix would solve this by asking people to test it.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.19%. Comparing base (991889b) to head (dc1b007).
⚠️ Report is 5 commits behind head on v3.4.0.

Additional details and impacted files

@@            Coverage Diff             @@
##           v3.4.0     #183      +/-   ##
==========================================
+ Coverage   99.17%   99.19%   +0.01%     
==========================================
  Files          15       15              
  Lines        2439     2489      +50     
==========================================
+ Hits         2419     2469      +50     
  Misses         20       20              

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