Although I haven't worked with a TOW replacement stock for a TC, most of the pre-carved stocks leave some wood where the lockplate will fit. This is usually around the outside of the lockplate and they leave some wood so you can inlet it for an exact fit with your lock.
As for material down in the cavity there are usually a few places where some material must be removed but this shouldn't be a lot of material.
I say that without seeing your replacement lock so I am guessing. If the stock was made for a TC lock with it's coil springs, and your new replacement lock has a flat spring it might need a whole lot of wood removed.
Also, because the lock was made by a different company, it may have material in places that the TC lock doesn't.
As for the flushness of the lockplate with the side of the stock, it should be flush or even slightly below the surface of the wood. This allows you to sand the wood down flush with the lock.
If the stock was made for a precussion (as most TCs are) it will have some wood in the way for a flintlock.
The hammer fall on a precussion lock is stopped by a internal stop built in to it. This stop is often the tumbler bridle.
Flintlocks usually have a notch built into the cock which stops on the top of the lockplate or bolster.
Look at your flintlock with the cock (hammer) down and see if it is stopped from rotating further because a area of the cock is resting on the lockplate. This is common with a flintlock, and usually doesn't exist on a precussion lock.
Because of this flintlock method of stopping the cock, the wood on the stock must be removed to provide clearance.
To determine how much wood needs to be removed, install the flintlock with the cock down and mark the cocks position on the stock.
Repeat this with the lock cocked, marking the position.
The amount of wood which will need to be removed is a little bit forward of the forward "down position" and about 3/32 behind the rear "cocked position".
The depth will be slightly less than the thickness of the lockplate so it won't leave a hole or gap down into the lock cavity.
The reason for removing more wood aft of the "cocked position" is because the cock must be pulled back further than the "resting" "cocked position" to allow the sear to fully engage the tumbler notch when you cock the gun.
Hopefully this makes sense.