[Flink] finalize checkpoint marks in the new Flink source implementation

[jto]

This PR re-implements checkpoint marks finalization after is was accidentally removed in #28614
Fixes #30539 and fixes #29902

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[Abacn]

checked that if revert the change, the added unit test failed with

java.lang.AssertionError
	at org.junit.Assert.fail(Assert.java:87)
	at org.junit.Assert.assertTrue(Assert.java:42)
	at org.junit.Assert.assertFalse(Assert.java:65)
	at org.junit.Assert.assertFalse(Assert.java:75)
	at org.apache.beam.runners.flink.translation.wrappers.streaming.io.source.unbounded.FlinkUnboundedSourceReaderTest.testCheckMarksFinalized(FlinkUnboundedSourceReaderTest.java:306)

anyone able to confirm this has fixed the issue? CC: @anartemp @gfalcone @noster-dev

[github-actions]

Reminder, please take a look at this pr: @johnjcasey

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.27%. Comparing base (c44b454) to head (280aadd).
Report is 131 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff            @@
##             master   #30849   +/-   ##
=========================================
  Coverage     71.27%   71.27%           
  Complexity     1485     1485           
=========================================
  Files           904      904           
  Lines        112898   112898           
  Branches       1076     1076           
=========================================
  Hits          80471    80471           
  Misses        30408    30408           
  Partials       2019     2019           

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[je-ik]

Ah, I missed this before #30971 was merged. I'll try to consolidate the two PRs.

[je-ik]

Closing in favor of #30987.