I do have access to these 2 excellent books but I guess I haven't been studying hard enough. 
The Japanese can be fanatical on anything that they put their mind to.
As for parts, how do service replacements affect these watches? I've heard that serious collectors do prefer the original dial and hands. However would a badly tarnished dial be preferable to a new service dial? Also will 3rd party replacement parts substantially affect the value of the piece?
Well here is where it gets a little complicated. It order to give you a clear picture. First we must establish a benchmark or criteria to determine the value of these watches.
The factors are
1. Rarity (numbers produce)
2. Wearability (those where the size are smaller than 35mm are not well receive)
3. History (own by celebrity, famous collector or represent an important event)
4. Availability (special issued, not sell thru AD or boutique)
5. Design (some are odd but attractive, some just plain ugly)
Not any one factor outweigh the others but it all goes hand in hand.
Now to answer your question if a model is seriously rare like the Sub 6200, factory service hand or even dial are acceptable because it's too rare. It will affect it value but not that much or rather the all original will command super high premium. However for a model that's not as rare the service dial and hand will effect its value considerably.
3rd party are often view as fake. Unless the parts are so rare that some enthusiast took the trouble to manufacture a new one that retain its original look. Then they call it aftermarket and these ain't the cheap stuff we found on the bay.
If we take the 5513/1675 as a case study.
My advice is never take an aftermarket dial because original ones are plenty to be found. Hands I can tolerate as long as it's make to look correct to the original.
As for servicing the vintage watch. There are 3 source that available.
1. RSC run by Rolex
2. RSC appoint by Rolex
3. Season watchmaker train by Rolex.
They all have their pros/cons. I personally found out that a good relation with a season watchmaker is worth the trouble and risk. Even they are often old and temperamental but they treat a watch like they treat their children. The have this pride in them. That's why we look for a season ones not a youngster and because they are season hence they're old. BTW 10 years experience is not season. My criteria is at least 15 years. We want them to be train by rolex because it will solve the parts issue. Servicing a rolex watch is not hard but getting the genuine rolex parts is. Only people in the circle know where the parts are located.
I find if even I brought a vintage rolex to RSC I ran the risk of having my movement5 and parts upgraded. The vintage movement is gone the tritium dial is relume or worse replace! The case is super polish and look new. Then what's the point of having a vintage watch. A vintage watch that look new is just an old model watch not vintage. It has no appeal. The history and memory of the watch is all erase. Sometimes I have no say to RSC to do it my way so I usually sort outside help.
To start I suggest a Sub or a GMT.
Why because they are plenty and price has not reach the sky ... yet.
I'll start by looking for a 5513. The interesting is the model has gone thru many face lift and certainly a joy to study the evolution.
The 1675 is where I will start. It's the same with the 5513 as it also has a long production life and gone thru many changes.
The pitfall are
1. Lots harder to tell fake from real.
2. Servicing could be an issue
3. Price gap between a fair and good condition is huge.
4. They are more fragile than new watch. (I know rolex suppose to be durable but these are 30~40 years watches 
)
There are some books to read but they aren't all that accurate so must be taken with a grain of salt.
I'll post some photos when I have time.
I agree that the Sub or GMT will be a reasonable starting point, especially the 5513 and 1675.
And the pitfalls that you've mentioned are indeed scary for someone without the requisite experience and knowledge. I guess one way to learn fast is to learn through one's mistakes.
Is Rolex service support still available for these 2 models that you mentioned?
Looking forward to your pics.
very informative. i learn another lesson even tho is abit late for me. everyday learn something new 
It's not too late to turn from the dark side. 
This post is long enough as it is. I'll post my reply in 2nd post for ease of reading.
Regard
Tyler
