Ok, first off, not sure if the lead section (top of page) should be 1 or 0.

But if I'm understanding correctly, for a page like:

( Issues in lead section and second section )

pageLoaded: {
 sectionNumbers: [ 0, 1 ] // all sections that have issues
}

// clicking on first section
issueClicked: {
  sectionNumbers: [ 0, 1 ] //  because section = ALL
}

// clicking on second section
issueClicked: {
  sectionNumbers: [ 1 ] // number of section that was clicked
}

Section i should correspond to the URL action=edit&section=i and section 0 is the lead.

The purpose of the section field is to let Tilman know where in the article it was clicked.
For your examples your understanding is correct with exception of all - clicking an issue in the lead where url is #/issues/0 or all would only log [0]

Change 454925 had a related patch set uploaded (by Jdrewniak; owner: Jdrewniak):
[mediawiki/skins/MinervaNeue@master] Log sectionNumbers in PageIssues schema

https://gerrit.wikimedia.org/r/454925

Change 454925 merged by jenkins-bot:
[mediawiki/skins/MinervaNeue@master] Log sectionNumbers in PageIssues schema

https://gerrit.wikimedia.org/r/454925

One minor issue remains blocking this from sign off : T202940

QA will happen as part of T191532

Blocked on https://phabricator.wikimedia.org/T203050#4564793