Hey and welcome!
The Tilemaps plugin for Duality does not support any other tilemap type than rectangular 2D tiles out of the box, but there are some programming interfaces available to extend its default behavior to a degree.
I've never done any isometric tilemaps myself so far, but I think
that for isometric tilemaps, the main thing that is missing would be an isometric renderer for the already existing tilemap data
and hopefully you can re-use the existing data structures and editor support already in place. You can provide a custom tilemap renderer by implementing the ICmpTilemapRenderer
interface in a custom component, which would take the rectangular data and displays it isometrically. This will require some knowledge about how tilemaps and renderers work in Duality, so I'd recommend to get familiar with the environment first - maybe implement an unrelated custom renderer according to the wiki article you linked to get used to working with them first.
When you proceed to write your own tilemap renderer, take a look at the default ones source code
to get a better idea on how it works and what the interface API does in detail.
As long as you stay on a 2D plane, physics should still work for isometric tiles, though you won't be able to use the default TilemapCollider for auto-generated collision shapes and will have to provide a custom implementation of that as well. However, since all that changes here are the shapes, you'll likely be able to reuse most of the existing components source code
in your own version. If you don't need auto-generated shapes, you should be able to use the out-of-the-box RigidBodies without problems.