Before the 3.7 Roadster kicked off I was in discussion at the factory - ( I was seriously considering a 3.7). There were a number of things going on at the time. If you recall, Roadster production had ceased, pending the new engine and there were a few weeks when no Roadsters were being built.
I was informed that there were some difficulties in negotiating the engine supply, and at that time the cost per unit was thought to be too high. It's also the case that the instruments used are tied into the ECU, so there were no other options for those instruments which split opinion.
Reading between the lines, it may have been a take it or leave it deal. When you have a company the size of Ford with the huge resources devoted to designing a capable ECU, it's understandable that it would take a high level of knowledge and ability to be able to enter that ECU and 'improve' it. Or come up with a replacement for that matter.