Absolutely not. Every ecu I've used has settings for single, double, staged or individual injectors, so you can set them up for a 4 cylinder. You can either specify at order, or configure (within certain limits) the trigger you want. The best ones are 36 tooth, but you can use 4 or less, with poor response. For a vmax something on the back of the gen rotor would seem ideal.
The ecu doesn't know or care what engine it is, especially for fuel. For ignition the v4 does produce problems, hence my suggestions for using Ford edis and the vmax triggers - however, the latest spec ecus can do unneven firing, and ultimately there are only 2 events.
So you don't have to completely program anything - either spec it on order or get one that can do the odd firing v4. Not hard, and probably quite fun?