Update: I realized there is another, easier way to get actual Jewel chao into this game for breeding purposes; download someone else's chao garden save file. GCI files will load straight up as long as the GameCube slots corresponding to the folders the files are in are set to "GCI" in Dolphin's configuration. For GCS saves, the Card Manager can be used to either import one into a RAW card file to use with the slot set to "Memory Card", or convert it to a GCI. For whatever reason GameFAQs is the only site I could find on the Lightnet that shares SA2:B saves for GameCube... the garden uploaded by "TheZeldaFan" has the largest collection, while this is still only a fraction possibly half of the full Jewel chao list.
Machines running Dolphin 5.0-6467 x64 onward:
#1 Windows 8.1 x64 | Core i7-4770 @ 3.4GHz | GeForce GTX645 | 12GB (4*3) DDR3 #2 Windows 10 x64 | Core i5-6400 @ 2.7GHz | Radeon RX570 (main) + GeForce GT730 (alt)| 8GB (4*2) DDR4
#1 Windows 8.1 x64 | Core i7-4770 @ 3.4GHz | GeForce GTX645 | 12GB (4*3) DDR3 #2 Windows 10 x64 | Core i5-6400 @ 2.7GHz | Radeon RX570 (main) + GeForce GT730 (alt)| 8GB (4*2) DDR4