Apply import formatting to files in the 2nd top level

[akihironitta]

What does this PR do?

This is a follow-up PR of #4242.

This PR mainly changes the config file for isort rather than the codebase so that future PRs can apply import formatter step by step as discussed in #4242 (comment).

(We have a similar list of files to skip pyright checks in .pyrightconfig.json)

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[codecov]

Codecov Report

Merging #4717 (f63920a) into master (9a5d40a) will not change coverage.
The diff coverage is 100%.

@@          Coverage Diff           @@
##           master   #4717   +/-   ##
======================================
  Coverage      93%     93%           
======================================
  Files         117     117           
  Lines        8937    8937           
======================================
  Hits         8304    8304           
  Misses        633     633           

[Borda]

@akihironitta great work, that is exactly what I had in mind :]