So here's the thing: what you're asking for is an entirely different proposition. A chronology asks the question "in what order did the events shown here happen?" (That takes detective work and occasionally a bit of Talmudic reasoning.) A reading order asks the question "what is the most satisfying order for reading these issues?"
That's a substantially more subjective question, and it has a few conflicting principles that can lead to possible answers. Should issue A come before issue B if it starts first, chronologically? How about if issue B ends before issue A--which one comes first then?
There are also times when it's much more dramatically satisfying to read stories entirely out of chronological order. My favorite example of that is Secret Invasion: without giving anything away, there are stories in the contemporaneous issues of New Avengers and Mighty Avengers that take place long before Secret Invasion #1, and yet reading them before rather than after the first time you read the relevant issues of Secret Invasion would make the whole project a lot less fun.
(For the record, my personal preferred reading order for Secret Empire is Secret Empire 0, the Free Comic Book Day issue, Secret Empire 1-7, Captain America 25, Secret Empire 8-10 and Omega, and then whichever of the tie-ins you think you might enjoy.)
