There is no problems with your bolts, what you have is the evolution of Savage rifles. Most of the changes were done for cost savings reasons.
Savage has changed their polishing procedures/finishing processes, this explains the finish difference. The now place them in a vibratory polishing machine.
The diameter of the bolt body, was to simplify having two bolt bodies, one for left handed action and one fro right handed actions. By undercutting the bolt body, now they only need one bolt body, and just flip it for left and right handed models.It will work in the older actions. With this change there was some internal changes as well. The cocking knob, firing pin, and some other parts are different, mostly for the new process in the bolt body.
The rear bolt baffle, ( What you have marked with the green/yellow arrow) is fine some are tighter than others, I prefer them to be loose, because it helps a teeny tiny big on cocking force needed to open the bolt.
The ejector pin holds the ejector in place, It cost more money for them to finish them flush, especially since ( as you have noted) has no affect on function.
Yes the bolt are completely interchangeable, with consideration to head space. The barrel needs to be head spaced to the bolt. Each bolt is different.
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