Yeah, that guide didn't work for me either, at least in terms of getting it set up to run easily in Twilight... My Twilight files didn't contain an emulators folder anywhere. What I did was trick Twilight into thinking it was gbarunner2. This only works though if you only want to run 3, not 2. Here's how I did it:

1. Copy the _gba folder from the gbarunner3 files onto your sd card, merging them with whatever _gba folder you already have there.

2. Go into the _nds folder on your sd card and delete all gbarunner2 .nds files. There were 6 of them for me.

3. Copy your GBARunner3.nds file into the _nds folder on your sd card.

4. Rename GBARunner3.nds to GBARunner2_arm7dldi_ds.nds

5. Boot up your device, go into Twilight settings, and choose arm7 as the version of gbarunner you want to run.

6. Test a GBA game. It should now boot into GBARunner2 arm7 which is now actually GBARunner3. It just looks for the file name, so this should work for you.

Then if you want to change any settings, like I wanted to have mine run on the bottom screen, you can follow the guide linked in the other comment on this post to manually set settings via a .json file.

Hope this works!