Source: CurseForge

it should be updated to put the tomtom points where the instance entrance is instead of inside the instances.

Allthough I definitely agree that the coordinates should point to the instance entrance, this will be a big manual job.
Since the the XY-coordinates are nested within 'coords' and that bucket has more uses, the maps assigned to these items are currently the instance map and not map of the zone the instance is located in.

For example Midnight's Eternal Reins currently has one of Karazhans maps. If you want to point to the entrance for Karazhan, then you'd have to add the map for Deadwind Pass to Midnight's Eternal Reins, because that is where the instance entrance is.
This raises some problems:

• Midnight's Eternal Reins would then, according to the GUI, be obtainable in Deadwinds Pass as well as Karazhan. Both entries would show up in zone for Midnight's Eternal Reins. And thus;
• Only showing available items in zone would show Midnight in Deadwind Pass

The display could partly be sovled with 'zoneOverride'. That can nest multiple entries in zone under one name in the main GUI. This would generate a lot of new locale entries, as all relevant instances would have to be added.
This does however not currently solve the display-text in the mouse-over tooltip, which would still list both Deadwind Pass and Karazhan

That's a good point, and one I hadn't even thought about when I logged this issue.

I guess the question then becomes, do we want waypoints to be decoupled from the zone display code (GUI) or is hacking in some override an acceptable solution?

There were some other issues with the display text, such as #283; ideally any modification should also address those concerns.