Based on what Audi mentioned during their press briefing, it sounds like the Porsche engine is designed specifically for Red Bull and Alpha Tauri and therefore Audi's engine will be designed for the chassis they will be powering. Trying to pool resources into a more "common" engine would have resulted in compromises neither wanted to encounter.
Audi has also announced they have cancelled their planned LMDh program for WEC and IMSA due to entering F1.
It's unfortunate they have canceled LMDh. I for one was looking forward to their entry into that class tremendously. However, I can see their reasoning for it. Can't enter F1 with only 1/2 a St. Pauli Girl.