I recently noticed the same thing. I had thought of doing a MTO of a boot, but was disappointed that with the disappearance of the 5th Street, Bayfield, and Promontory Point Boots, options are incredibly slim.
The Dalton is a high-boot and I suppose it might be possible to ask to make a whole-cut version of it lacking the wings and broguing... that is, one could conceivably MTO a Shaker Heights clone from a Dalton, minus the tweed.
The Cronmok style might make for interesting MTOs, but it's unstructured. That could make for interesting suede, but limits my interest for leathers.
The Dundee is already shell cordovan and all the interesting shell options (such as walnut) are off the table.
The Bellevue is available and has a few options for an MTO. Brass eyelets, removal of the broguing, and better sole (mini-lug at least, allowing one to replace the heel-lift). Beyond that, it isn't a complicated shoe, there isn't much else to change except the leather.
There is no longer a viable, structured balmoral boot. There are no cap-toes.
I only hope this means the fall introduction of a new line of boots...