MSI V3.0 standalone

What controls the afterstart idle air?

The engine cranks, then fires, then the RPM surges up to about 2000 for a second or so, then settles back to whatever idle speed is set for that temp.
What controls/affects that post-cranking RPM increase?

 

So far as I'm aware, there is no specific after-start idle. You've got the one cell (under "More Settings" ->"Idle Control") where you can specify a fixed cranking duty cycle for the IAC valve, and after it switches from crank to run, I'm pretty sure it just starts seeking whatever target is appropriate for the temperature.

Try reducing the Cranking(dc) value a bit and see if that makes a difference.