Why are the mods not being done at the factory ??
While I know nothing about these specific aircraft or what the mods might be it is not unusual for customer mods or options to only be done after delivery.
Examples would be Boeing 767 winglets - you take delivery of a brand new $200m+ aircraft at Seattle then do one flight to where-ever it is they take a disc cutter to the wing for 16-20 days. Or the crew rest area on the 777 fleet, one flight from Seattle and into the hangar for several weeks to fit that customers specific choice.
An analogy would be wanting a particular car stereo that Ford don't offer. Once you own the car you can go and rip the dash apart as you please but Ford are hardly going to let you do it in the factory.