At what point do you RISK the shot or your hunt for an exceptional animal is the answer?
Yes, with some work and money, many factory guns can be made to shoot sub MOA and many around .5 MOA with careful load work up and good bench techniques. I have seen a 5R in 308 shoot in a 1000 yard Factory class that shot groups that beat 90% of the customs THAT DAY for regular BR guns.
I am a big proponent of the custom route after spending a lot of money converting 700s over too many years. The 700 has one huge flaw in the magnums that has bit me twice on hunts and that is the riveted extractor broke and I basically had a single shot. I had to carry and use a cleaning rod to remove the cases. Was it just the twists of that gun or what, but I will not go that route again. Switched to a PTG bolt and I would trust it anywhere now but it is not as smooth as my customs.
When it is all over with a "fully reworked" 700 will cost as much as a custom and be worth half and be half as smooth and reliable. Yet you can add a good trigger, bedding, lug work at least and stand a 50/50 or more chance of having a good shooter for most people.
Got to admit, for a cost conscious hunter that wants as close to custom as he can get, the Savages are a pretty easy way to go. Pre fit match grade barrels, decent triggers, and changeable bolt heads certainly allow many options with rifles that are very consistent shooters as the norm to start with.
I have and have had numerous sendoros that will more than work with bedding, trigger, lugs etc without full action jobs. Just will not trust the Remington magnum bolts anymore though for serious hunting guns without changing to a PTG bolt and M16 extractor.
If money is not the object, obviously go with the custom and never look back. The smoothness, and reliability are a huge factor when it comes time to pull the trigger. However, If you are shooting 500 and under, you can tweak numerous factory guns to get you there. I just shot two deer Tuesday with a 6 lb worked over Model 600 Mohawk in 7-08 factory mountain rifle barrel on it and with Edge stock that shoots 3/4 to 1" with my old standard load of H414 and 120 Btips and that is plenty for what it is designed for.
As for the numerous "internet magical 1/4 MOA" guns, the shooters at BR central have had a standing offer of $500 to anyone that can bring one to a BR match and shoot 5 consecutive 5 shot groups of .250. Last I knew, no one had ever collected that $500 yet. I have watched friends change guns and barrels like women's dresses to find that exceptional good shooter for factory class guns in matches.
We have all shot an occasional wonder group, but that does not make it the norm.