I believe that ndstation will just pack up the .gba, a loader, and a few other files into a .nds file so that running the .nds will load the GBA ROM onto the EZFlash 3-in-1, but the GBA ROM itself still runs on the EZFlash 3-in-1. So, if you're asking if the .nds file created by ndstation will run without the 3-in-1, the answer is no.
Rudolph's GBA ExpLoader seems a lot easier since you don't have to go through the extra step of packing the GBA ROM into a .nds file and presumably the .gba file is significantly smaller than the .nds file created by ndstation.
-Bri