"New" Marker for Comments does not vanish
Trying this out in vanilla Bartik doesnt have issues.
I couldn't say for sure without looking at your "modifications". But on digging a little deeper I assume it's one of the following

The reason for your issue is most likely your modifications to node.html.twig(or node--article.html.twig)


You would have rendered 'comments' outside of 

&lt;article{{ attributes}}&gt;
&lt;/article&gt;


in your template.
You would have removed a required attribute "data-history-node-id"
from

&lt;article&gt;
&lt;/article&gt;


tags in your template


Details:

/history/NID/read always returns the current timestamp

The module in question here is the new core 'history' module.
The path "/history/NID/read", if you check history.routing.yml, resolves to readNode() in HistoryController
In there you can find a call to 
history_write($node->id());
first and then followed by a call to 
history_read($node->id())
which would return the current timestamp (because it has just updated it in the previous history_write line)

According to the function description


  "Marks a node as read by the current user right now."


so it is used to mark a node as read by the user and not to get a node's last read timestamp.

The new marker logic is at core 'comments' module
comments/js/comment-new-indicator.js
processCommentNewIndicators() function.

The following line will not return a value

    var $node = $placeholder.closest('[data-history-node-id]');



if the $placeholder(marker) was not inside  tag with attribute "data-history-node-id"
if the article didn't have the attribute "data-history-node-id". Make sure you don't remove it from your node.html.twig (or equivalent)