Don't mean this with any disrespect, but are you low level trolling? You seem to be coming back with question after question, some of them with relatively straightforward answers I would have thought.Two more questions, if two dark/grey pads (like on the photo 1 here in the old frame) are removed from one side of the side window panel (which is not ever going to be opened, like on the photo 2) to the balcony doors is it ok or not? And if the level looks like on photo 3 in one place is it ok? Should the level be used when fitting windows?
Should new handles be scratched or damaged? No. Ask installer to replace.
Should new glass be scratched or damaged? No. Ask installer to replace (or negotiate money off assuming it's just scratched not cracked.)
Should doors be difficult to open/close? No. Ask installer to adjust and if still too difficult and can't be fixed, request reinstallation.
The grey bits you refer to are packers, used to ensure glass is correctly installed. How do you even know if they are/aren't installed in the side panel? Once glass in and beading on, you can't see them?
If you think any of the frames are quite significantly out of plumb, speak to the installer and either negotiate money off or request reinstallation.