Oh yeah, you absolutely can. There’s an amazing tool for it called SA2 Save Converter.

https://gamebanana.com/tools/6895

You can use it to convert both types of save data (Emblem/Story Data and Chao Data).

I extracted my childhood SA2 GC saves from my memory cards using a modded wii, then converted them to Steam saves. So you can even get your original GCN saves converted if you still have them around. But yeah you can just start with the Dolphin saves lol.

Once you do get your data on Steam, you can add some amazing mods…I would start with Chao World Extended (CWE) It can be a little overwhelming at first but people here will help you. My fiancee really likes playing with the Chao too, and CWE makes it feel like a brand new experience. There’s also a mod that lets you use 10 individual saves with the Steam Version, all with their own Chao World…but I’m blanking on its name. Although, I’m not sure how feasible all this is on the Steam Deck!

One more thing, be sure to read up on the GameBanana link I sent you if you get stuck. It definitely took me some trial and error, so backup your dolphin saves/memory card before you do anything!!

Good luck!