Sorry I didn't update this earlier – I've confirmed that the fix for those issues (8de940b5) also fixes this bug as well. These changes should be deployed next week. I'll also add a test case based on this to our code, because (on second thought) it looks significantly different.

Note that the fix actually disables the reply tool for the two comments adjacent to the template :( (if you click [reply], you'll see an error as described here). I hope that this won't be a common problem, as usually that template is placed at the top of the section, where it doesn't cause issues.

Change 753865 had a related patch set uploaded (by Bartosz Dziewoński; author: Bartosz Dziewoński):

[mediawiki/extensions/DiscussionTools@master] Add another test case for transclusions overlapping comments

https://gerrit.wikimedia.org/r/753865

Change 753865 merged by jenkins-bot:

[mediawiki/extensions/DiscussionTools@master] Add another test case for transclusions overlapping comments

https://gerrit.wikimedia.org/r/753865

In T298408#7621419, @matmarex wrote:

Note that the fix actually disables the reply tool for the two comments adjacent to the template :( (if you click [reply], you'll see an error as described here). I hope that this won't be a common problem, as usually that template is placed at the top of the section, where it doesn't cause issues.

I realized that this can actually be a improved with a small change to the template. After this edit: https://commons.wikimedia.org/w/index.php?title=Template:Tracked/layout&diff=prev&oldid=623427999 all comments on https://commons.wikimedia.org/wiki/Commons_talk:SPARQL_query_service can be replied to, without causing any page corruption.