I have the same error when it's trying to resolve path aliases.
For my case, i add --project tsconfig.json in the command to load proper config and it works.
In your case, it would be:

"typeorm": "ts-node --project tsconfig.json -r tsconfig-paths/register ./node_modules/.bin/typeorm"

... or you can create another tsconfig file e.g. tsconfig.typeorm.js and add --project tsconfig.typeorm.json in your command.