That will be a project! You've got my respect for taking it on.
What size console are you going with? If it's wider you'll end up screwing the top to the stringers. If you go with a narrower one you can install a hatch inside which will give you access to through bolt it with backing plates.
Some people glass aluminum plates to the underside of the deck and thread T top fasteners into the plate. Following Dirtwheel’s lead, I chose to glass solid fiberglass pads into my deck for a corrosion free version.
I will have to look into the t-top fasteners that you reference.
You'll hear some strong opinions (from both sides) if you plan to cut the transom off completely. It looks like it's not completely flat across the back so you may not have many options if you want to raise it up. I personally would not do it but that's not to say that it can't be done. I would just do lots of homework on each option before you commit.