If you can't clean up the painted edge, you could always add a 1x3 piece of wood as molding. You can even carry it up to the ceiling to frame that wallpaper. I don't see that paint color in the wallpaper, or maybe it's a lighter version of the flower centers. Maybe stencil on a design using the darker color, or another color from the wallpaper to help tie it together. Then narrow floating shelves or vertical frames or something in the painted areas it you feel you need it. Maybe turn the bed around so the wallpaper is the headboard.

I agree with divadeva. More lights. If you can add pot lights do it. If they're already there add task lighting and up the wattage on the bulbs on the pot lights (replace with LED and you can make them brighter because the wattage on LED is lower for brighter light). If you have all of that add decorative lighting. If ventilation is an issue find a way to move the air around or add air filtration. Maybe the HVAC is deficient. Maybe you can add a HEPA filter instead of the standard one that comes with the unit. Call an HVAC specialist to see if there is a way to boost air flow in the room.

The amazing thing is that you have the luxury of approaching the architect about these issues. Laminated glass should address the security along with any alarm or security system you plan on installing, though the laminated glass may have size limitations. Regarding the waterproofing you should contact the architect, contactor and waterproofing subcontractor, or see about hiring an independent waterproofing specialist who can detail and warranty the condition. As a design consideration, make the lower area a garden or gallery or sculpture area and upper should be all glass. Maybe a garden roof there too if accessible or visible. In any case looks like an amazing place!!

Suvarchala, I am presuming that you do not want the doors to face each other due to privacy concerns. If that's right you wouldn't also want the guest/visitors to go to a bath in one of your rooms. Have you considered that before dropping off a common bath from the plan. If your neighbour has a door facing yours then you can also think about doing a mirror image of what respected member suggested above. I.e. door on the pooja room corner instead of the guest room corner. Thanks, Nitin CORNERSTONE DESIGNS Bangalore