I guess its a moot point since you have abandoned the idea. But just in case you are still curious, I can give a couple ideas about it.
The emulator is generally compiled from portable c/c++ code with an arm cross compiler and/or written in asm for arm processor. It is linked into an elf format shared library (GBCoid contains "ELF 32-bit LSB shared object, ARM, version 1 (SYSV), dynamically linked, stripped" ). The resulting library is saved as a .so file. [google 'android JNI' for more info]. An apk file is just a renamed zip file that contains a certain directory structure. When you install an apk, it is basically unzipped and files copied to your phone. The emulator library is one of the files stored in this zip.
This is where you have a couple different ways to bundle the emulator and the rom. One way would be to include your rom in a char array compiled within your .so library. Since you are always loading that same exact game, you can have it like that and just memcpy() it into place when you need to reset, load, or similar. Another method would be to include your rom in the apk in /assets/my.rom and then hardcode the path in your program so it always loads that file. Then creating different game-emu bundles means you dont need to recompile any c code as it will be exactly the same. You only need to change some strings in the xml files, your icon images, and the rom you include in your apk.
If I were doing your project, and I wasn't making any specific changes to the emulator for certain games such as custom control layouts, then my decision would be based solely on my laziness. I would start out by using the char array method because it is the easiest. If I was only doing one or two games, then the effort to change that char array doesn't become much. However, if I then decide that I like these things and I want 20 of them all with different roms, then the hassle of editing that char array gets to be a bother. I would say that after about my 3rd or 4th bundle I would probably invest the time to include the rom separately in the apk and load it at runtime.