The tutorial doesn't explain this very well but the 'rsdk file' folder is just a backup spot for your data.rsdk file instead of deleting it, and not where the data folders go. If the data.rsdk file is in the correct spot it won't go into 'data folder mode'.
Move your Data.rsdk file into your 'rsdk file' folder.
Move your 'Data' folder into your 'Sonic1' folder.
Delete the 'Bytecode' folder.
Download the 'Scripts' folder from here, and extract it into your 'Sonic1' folder.
Also you can put your Sonic1.3dsx file into the 'Sonic1' folder, but it doesn't really matter.
It should look something like this at the end.
View attachment 245345