"But now I will have a mismatch of trim as I would probably put more of a craftsman style simple block trim around these new sliding windows"

Save the existing trim by removing it carefully or visit a real lumberyard looks to me to be either a standard colonial casing or a beaded colonial casing, cannot be sure because of the angle.

Really we have no pics of anything that can be commented on. I assume you want this to be a wall of doors to the exterior but I need to see the whole space. You say modern but in my head bullnose trim not modern . I need to see more .

You can trim out the doors in a variety of ways. Frankly this door systems are so $$$ I can't see the advantage unless you live in an area with no flies or rodents.

Here are some more photos of the space

I'm not sure what your view is on the other side but a two-panel slider would offer less visual obstruction than any folding door system with multiple panels. Not to mention, the performance/air-leakage of folding doors is sub-par.

As for the molding, I would have it carefully removed in the hope to reuse it after installation.