Luce, my EE schooling was minimal and almost 60 years ago. Even worse I have not used it for almost as long. As luck would have it (usually) I can sneak around the need for having to use any of it. All the points you are making are valid but if you stick within the SAE spec, virtually all the EFI systems will provide the tables and screens to use the data of the SAE spec characterized injectors.
Some do better jobs than others. Megasquirt is impressive in the extreme for their thorough approach to the characterization issue. They also allow you to ignore it if your supplier did not provide the characterization data — very nice save there.. Max power WOT tuning is not particularly challenging. Part throttle, off idle, coasting, decelerating and then accelerating, and proper accelerator pump enrichment schemes are much more challenging.
The electronic redesign of a system is not always the shortest way home when you are attempting to tune an engine. If the basic design falls short of the mark for specific purposes that are important to your build, it is usually less expensive to buy a different system that handles the particular issue more to your liking than re-engineering the one you already have.
Stay inside the sand box the manufacturer supplied and pick a manufacturer that provides good tuning tools inside the SAE fenced in playground. Everything becomes easier when you do this.
On the other hand the Megasquirt systems provide the code logic so you can get creative if you want to. It is just a matter of deciding what's most important and how big a chunk of work you want to bite off.
My EE skills are old, rusty and dull so I just buy the box and stay inside the sand box to play with tuning. For those with the prerequisite skills there is absolutely nothing wrong with going about re-engineering portions of the system you want to improve.
My old hands are full just doing the tuning
Ed