In my opinion, the biggest drawback of pre-inletted stocks is that the barrel and lock position are fixed and can cause problems with the remaining geometry, especially if you want a different pull. I prefer to lay out the barrel the way I want it, lay out the lock, then lay out the trigger prior to drafting in the butt stock geometry. You just have far more freedom in geometry and shaping.
The other drawback of pre-inletted stocks is that they are usually set up for a particular barrel, lock and buttplate configuration. If you'd like make your own buttplate, you may be very constrained. I'd much rather make a buttplate and then shape the stock to match than vice versa.