I doubt ordering a 744 without autostart cost more money than one with it.
This is the very reason that operators like CX (which have now retrofitted it on some RB211 744s) and SQ (PW4056) do not have it.
I read a post from a SQ 744 pilot a while back, and he said that it took them far longer than any other 744 operator to start up all 4 (when following their SOP) with manual start(saved the bean counters $$$) In fact he said that in frankfurt and london ATC were getting pretty annoyed about the whole thing.
Maybe somebody from/ex. SQ can tells us more about it?
So when it comes to autostart I am certain that you will pay more to have it then not to have it.
However there are some non-standard customer options that will cost you more.
For example:
QF ordered their RB211 744s without taxi lights, only with runway turnoff lights on the nose gear (just like many other operators did) however their last 3 744s with RB211s had them and so did their 6 744ERs, this because boeing decided that with taxi lights was the new standard and without them would cost extra $$$.
Or LH, which have all the light switches the other way around on their boeing fleet. Pull the switch and it's on, push it and its off. This cost extra $$$ too as it is non-standard.
The classic 747 had even more differences I hear.
And for this very reason no boeing type is the same until you enter the cockpit.