When you are exporting for VTT use and plan to use grids, make sure to always export using the rectangular section option. For example, if you look at your screenshot above, you'll notice that you have a border outside your map that is part of your image.

CC3+ isn't a "grid mapper", so export sizes are for the entire drawing, not just the gridded areas, so when you export the image in a size of 2000x2000, that border is going to eat part of that size, not leaving a full 100px for each grid square. But if you use rectangular section when you export and make sure to only export the map itself (use snaps on when defining the area to ensure precision) you should get the right size.

It is also important to set the export size correct in both dimensions.

Well, since the map is 40.5 hexes tall, you can try to export it setting the height to 2025, just set the width to something ridiculously high, like 10000, and then make sure the crop image to aspect ratio is checked, this way the width will end up being whatever it needs to to fit the specified height.

This should end up with a file that is 50 pixels for each hex, measured by the hex height.

The maps are now in the atlas. Thanks for the contribution @Wyvern

Note that CC3+ do also have non-drawing entities that you can't find in the drawing window, but still lives on a layer and blocks it from deletion. Map notes are one example that comes to mind. And there is no user-facing UI to figure out which entities these might be.

The map have now been added to the atlas. Thanks for the contribution.