Typical examples of using Sitecore JSS with TypeScript involve using ts-node for the manifest generation process to compile manifest definition files. ts-node uses standard node resolution process to resolve modules, it does not respect the paths property from tsconfig.json which is a TypeScript compiler feature.
If you want to use the TypeScript compiler path mapping feature for manifest generation, it is recommended to use the tsconfig-paths library: https://github.com/dividab/tsconfig-paths
Then you simply need to register tsconfig-paths in config.js when you register ts-node and be sure they are both configured to use the same tsconfig.json file. This can easily be done by setting the TS_NODE_PROJECT environment variable.
Also be sure that the paths and baseUrl properties are properly set in the tsconfig.json file you use for manifest generation. Manifest generation is a separate process from building your JSS+TypeScript app, so it will typically make more sense to have a dedicated tsconfig.json file for manifest generation as opposed to extending the tsconfig.json used by the app.
/src
sitecore-config.ts
/sitecore
config.js
tsconfig.json
/definitions
something.sitecore.ts