Thanks for the responses,
Its Bizarre that they wouldn't allow you to book the visa as part of "manage My booking" after initial booking as adding photos and other details were taking a lot of time for 5 pax and I went ahead to buy the tixs without the transit visa hoping i can add it later on.
talking to Customer care and writing to their back office team did not help either with standard reply being it has to be bought with the original booking.
Any one actualy tried using visa from a different/dummy PNR to fly on a stopover flight booked without the transit visa..?
Worst case I'll have to spend $120 per person to get visa on arrival defeating the free transit visa promo.