The endgame may be too many steps. Here are some ways that may or may not be fun to do instead.

The way you need to grab a waystone, click map device, click area you want to go into, place way stone, open the map, go. It's like 2 more steps than it is in poe1. And too many clicks without action is not fun.

If you want the atlas to be a big "open world" as it is now. Then i think you need something different than waystones (maps).

Here's a few suggestions, that I just thought of now:
Maybe treat the atlas like you would Delve. Have the areas drop a resource (could be gold), that can be used to fund which tier of monsters the next area should contain. Fx t1 = free, t2 = 1000 gold, t3 = 2000, t4 = 4000, t5 = 8000 etc. This could litterally also just be waystones, but in a automatically picked up and stashed form. That will just automatically be consumed whenever you enter a new area.

Maybe have the content grow in difficulty the further away from your starting point you are. Atleast that way you would also feel like you are progressing towards something. And then let the areas be refarmable, maybe after we've moved 3-5 spots away from it, let some new monsters and encounters take over the area. So we always have access to a low level area, should we need it.

Maybe have parts of the atlas randomly be taken over by a monster type, like areas in poe 1 could be influenced by the shaper, visually this could look very cool to see implemented in the new atlas.

Maybe have the towers be the sources that influence the world around it (more then it does now), put in a waystone, tablet etc into a tower, and then let the areas around it be available to run without spending new resources on every single area you want to enter, so you craft one big thing, and then you get to run that thing x amount of times.

or if you really like it as it is now, let us have access to the stash tab while we are looking through the atlas, so we can more easily pick up a waystone, tablet, craft it etc. while we are looking at the areas we are about to farm.

Anyways, these are just from the top of my head, do feel free to add, remove, discuss, discard. But, I do hope some of these ideas send out some sparks of creativity to fuel the end game, what ever it may become.

Keep up the good work.