I see the confusion now. In my testing, in the item detail page, when I make the change in the visualization tab (and save it), it changes it in both popups and the data tables, regardless of where they reside. (as one would expect)
It appears as in your example, it only changed it for the popups, and tables in the visuallization tab, but, the in the data tab of the item details, it still shows the separators.
Not sure if you are using a view of a hosted layer or something, or why it would behave differently. I tested on two different hoseted feature layers, with both Chrome and Edge, and behaves as expected (either show thousands separator or not across the board).
Sorry can't be more help on this one, but looks like another of the inconsistancies of AGOl.
If just a hosted feature layer, I'd try re-publishing a separate copy to test and see if something went weird with your layer. If a view, update the view, make another view and test.......
Hopefully someone else has ran into this issue and will chime in here and get it figured out.
R_