I use the Skyrim Mod Organizer and SKSE.

The http://wiki.step-project.com/Guide:Skyrim_Installation#tab=Hacks recommends that I configure SKSE by manually creating Data/SKSE/skse.ini. I have done so in my vanilla Skyrim folder.

Given the fact that I always launch Skyrim by triggering skse_loader.exe via the Mod Organizer, will the skse.ini file be processed when it's located in the vanilla file structure (where skse_loader.exe is), or do I need to place it in the Mod Organizer's alternate file structure?

Yes. As long as you don't have another skse.ini file floating around in your MO mod folder, the game will use the one in your Data folder.

I see, thanks for clearing that up.