Zinc roofing has become fashionable but decent zinc roofers are few and far between. With rooflights, you often need to solder. I would stick with what you have, get the facias, flashings and gutters on and the rest of the outside complete with scaffold away before the end of summer. Get a new zinc roofing contractor and get your windows and doors ordered and fitted.
The L shape is loads better. The original plans based on a rectangle made no sense for the shape of the site. You can modify the L shape to suit the space you need. Sensible to build min 1.0m from boundaries.
You need some decent floor plans developed from this. Don't get too hung up on the garage.
The principal of building a house is already agreed. What was on the outline application? They normally have some sort of drawing, so they could see what was being asked for in terms of no of storeys and bedrooms and proximity to boundaries.
Lose the porch if it upsets them. Just do a reserved matters application and don't make it controversial or flash looking. I would aim for about 1400ft2.
Have a look at
If the red line is the boundary you would need to get an easement from the neighbour to allow fascia and gutter overhang. You may do better with an l shape on both floors by going further back for part.
+1
Allow for wider external walls. More storage, less glass.
The space is so small you will not be able to move around. You need some ventilation up there but it is not obvious how to do this. Is this going to be habitable space?