But for your first portable, do you really want to be trying to cram it in as small a case as possible? No, you wouldn't, unless you are experienced with similar stuff or insane. That said, I could have easily fit my YAP64 into the ZN-40 if I had smaller batteries. Probably an external cart slot or just the cart slot on top, but it would have fit. I could have built it into an AG-85, but then I would have to drop a lot of my planned features, trim the board more, and use different batteries.
That said, there are plenty of other enclosures that could be used if you are creative. I think one guy used a Linksys router. The ZN-45 is same old and lame, but it does work, and it's fairly easy to fit an N64 in.
Or a Yobo.