That is a beautiful space, if it were mine I would insulate it and make provisions to heat it so that in winter it would always be above freezing. Also make provisions for cooling so that you can use it all summer, or cool it on warm winter days. Exhaust fan and intake vent low down for cooling. I also would not try to block out light, maybe shears but that is about it. If you keep it between 25 and 40 F you can use it for winter storage of hardy trees. If you have light coming in, if an Eurasian species wakes up early on you - you can simply move it to a window. I would make it primarily a nice work space, relegate storage of chemicals and 'ugly stuff' to a shed outdoors or the garage, make this space a living space. On the shelves display pots you don't have trees for yet. Your work bench ideas sound good.
But if it were mine, I would gear the space more for the storage of sub-tropicals, and make it a comfortable work space. I would keep it heated to maybe 40 or 50 F at night, kick it up to 60's in the day and use it as a year round work space. You could then enjoy trees like Citrus and Camelia and all manner of sub-tropicals and some tropicals in comfort. I winter most of my natives on the ground under their benches just covered with a tarp. They can take the cold, so don't need a special structure. This space is too nice to be tasked to just storing trees that could be on or in the ground for winter.
Those are my 2 cents. But what ever you decide to do I'm sure it will look nice.