I’d delete the high windows on south wall in new extension as you have a large western window. The north side in dining area should be a standard window. Consider your window furnishings. Not sure what you mean by window below ceiling.
Ensuite - the toilet is hidden behind the door which is ideal. But I don’t see anywhere for towel rails except in shower. You will need shutters or blinds on window

I wouldn’t do skylights in bedroom and they need regular rooftop cleaning if you want to see the sky. Skylight in the hall where they intersect would be good

Your new floorplan looks great, because of the close proximity to both North and South boundaries I would keep all highlight windows for privacy, light and cross ventilation. These windows while providing all of this also allow for better use of space with furniture placement being able to use those walls. Simple fitted blinds will be easy to use. I would also consider adding one to the Lounge room instead of the skylight which is West facing, the current small window will need either of these. Your ensuite works well and towel hooks can be added in strategic places, I personally prefer these to rails, wet towels from the ensuite can be sent to the laundry to dry in the dryer, plus the half windows could have a towel rail placed below them

Adding highlight windows above stacking/sliding/bifold doors is normal or having taller doors, keep in mind that these doors face west so external protection will be needed

I wouldn’t add a BASIN, I think that is what you meant, to the toilet in laundry, you described as social toilet? You have the laundry basin in the same area, this can be used for guests.

I assume this what you meant regarding having window between ceiling and sliding door. It’s usually called a transom window, and will depend on how high the ceilings are in your building, and how high the sliding doors are.

I’m assuming by “social area” you mean the Living and Dining, with the sliding doors going to outside patio area.

Leave the ensuite as is. Toilet is hidden, and shower is private. Basins are used more, so easily accessible.

You could install floor to ceiling sliding glass doors from living and dining to patio. This would be more expensive as structural supports would be different to current plans.