I get your point about getting invested in the save file. If I have to launch the emulator on PC, choose the ROM, make sure the controller is fine, and make it full screen. I'll never launch it enough times to finish a long game. The trick (drumroll) is to run emulators on a game console like a Switch. Some titles I put an icon on the home screen with the box art (forwarder) so I forget it's even a thing, just press A and play.
The original headache that pushed me to emulate was my save going poof halfway through RPGs, twice. And instead of worrying about batteries, decided to start it over on Wii virtual console. Of course, many old games don't even have saves, but I prefer a sleep button to worrying that a light breeze will freeze the console (this still happens to me lol) so I'll only turn on my Genesis if I'm in the mood to see a perfect dithering effect, otherwise I just want the path of least resistance to a few Sonic levels.
Put it this way, it would suck to lose the Dreamcast but I'd retain access to my favorite games on it. But if I lost the 64 it would effectively break my ability to play it. I have considered getting a USB adapter for the controller, or just the official Nintendo wireless one, but then it's also a multiplayer console, you need a mess of controllers, not all our fav mp games are on NSO and some develop issues in split screen when you do it yourself. So yeah, I don't want to lose any, but if I had to choose one to keep, 64 hands down.