This is a First-Class question, one I am sure that others have wondered about themselves.
This is the good news and the bad news. With a carburetor through study and experience you learn that certain symptoms come from certain sources. You use the knowledge to logically make a diagnosis by troubleshooting. Then if it is a carburetor like the Enfield, you fix or adjust what is wrong. With an Enfield you can buy parts unlike many newer carbs so you don't just have to replace it.
With EFI the entire fuel deliver system and engine timing are controlled by a computer. It measures several different inputs including air temperature, Oxygen levels in the exhaust, throttle position, engine timing, engine temperature, load etc and delivers the exact quantity of fuel for each situation micro second by micro second. The process is so complicated that when a problem appears it is all but impossible to diagnose it in the conventional sense. With no tools you start replacing items blindly until you happen to fix what the problem was.
With the built in diagnostics or a specail computer tool the system itself will tell you what is wrong. To your point each sequence of blinking lights will tell you which part is defective,. If it is more than one part it will tell you that as well. If you identify the problem part the first thing you do is verify that it is connected properly and if that is good you replace the part. This will save you tons of money blindly replacing parts and it will tell you with no training or special tools how to fix your bike. It does remove some of the "art" out of diagnosing problems, but on the other hand it can help a relatively untrained owner an expert. For the most part EFI is very simple in concept. Most companies make it a mystery.