The problem with this thread is that we are still left guessing the requirements.
Debates about choice of database might be “putting the cart before the horse”.
In first post the OP writes “my app and database are completely offline… no servers or networking”.
But now we learn “is the data inside the database safe when the application is shipped and installed on the user’s machine?”.
These are shifting sands.
Based on this opening requirement
“BTW the kind of data is not quite large (no videos or photos,… only textual data) BUT there will be some heavy mathematical computations while interacting with different sorts of data distributed at different places”
and this last requirement
" i want to interact with the data file on the long-term"
although I still remain in the dark about the real application I would review development plan.
The predominant requirement seems to be “heavy mathematical computations”. Database is less important and could be a simple local user SQLite3 database for all we can deduce so far.
Switch to developing a Shinyapp which can be deployed to users in a number of ways:
This gives the OP central control over the app and ShinyApp is ideal for “heavy mathematical computations”. If the end users are not too technical the ShinyApp could be placed into a UI wrapper (including Electron or Python) to orchestrate the local setup.