they put the minimum order so that you cannot order less than 2 person. they probably have an overhead they need to cover. its just like Nabe, it does not matter how many ppl u have, you have to order minimum 2 person share.
so yes, u can order 2 person portion shared by 3 ppl. They need to give unit cost per person so that if someone wants to order 3 person or more, they can just multiply accordingly.

no

If NRT, MAS uses 777-200 which the capsule type seating, not 100% flat, its tilted at an angle, but still can sleep. timing wise, MAS is good, as u leave midngiht reach there 6-7am... just intime for you to buy the special NEX + Suica from JR

Cathay, if I am not mistaken, the Leg from KUL to HKG, its on an older Airbus... and u dont get the flat beds, but if you are lucky then u get the 1-2-1 business class with flatbeds... those are better than MAS.

Not familar with JAL business class as I never flew before. my recommendation, is MAS... if the tax and surcharges are the same.

Haneda is much better than NRT... much nearer and you can take local trains.... again, check ur arrival time vs train avail.

you are right, i have not been to Tokyo since 2012... now only one way 1500...which is quite cheap too... but no return discount.