Target actions are made exactly the same as all of Savage's other actions. With the new machines they have now the face of the receiver typically only has a variance of 0.002" or less. The face of the bolt head will be slightly dished from the tumbling process - same as any other Savage. Recoil lug that comes with the target actions is precision ground, not stamped like is used on all the non-Target grade guns.

So the real question you need to ask yourself is this: Do I want to limit my aftermarket options building with a Savage, or do I want to go with a custom to maximize my options?

Answering that question best for your needs will depend heavily on what you're building the rifle for - which you never stated.

If you're building an all-out competition rifle, a custom 700 Rem based action is the way to go as there are far more trigger options available - especially if you're shooting benchrest or F-Class and want it below 5oz. I would also recommend the custom action for a PRS rifle simply due to the Savage being somewhat finicky when to comes to extracting/ejecting the more popular PRS cartridges (6x47L, 6.5x47L, 6 Creed, 6.5 Creed, etc).

If you're building a custom hunting rifle, a Savage action would be more than adequate - with some exceptions depending on cartridge of choice. In this case however I wouldn't both starting with a Target action (unless it will be a dedicated long-range varmint rifle) and instead would just look for standard centerfeed action and put that extra $$ towards a better barrel or stock.