Yes, the flow is from top to bottom.

Disembarking passengers exit first and go down stairs to arrivals, which
is usually underground to connect with subways. Transit passengers are
redirected to departure hall which is above the platform. The turnstyles
for departing passengers are not opened until the disembarking passengers
have exited the train on their way to the lower arrival level.

I'm still not seeing eye to eye with you on this.

Let's take the two main scenarios:

1) catching train at origin station
In this case, incoming trains typically sit on the platform for at least 45 minutes before leaving (because they need to be cleaned/maintained). By the time departing passengers are permitted to board, disembarking passengers are long gone... actually, many of them are probably standing in an endless taxi queue, but I digress.

2) boarding train at station stop
Boarding passengers are always permitted to stand on the platform before the train shows up. In fact, since the average station stop is less than 2 minutes, anyone not adhering to this protocol would probably be left behind.

Revert to the OP's questions
http://www.flyertalk.com/forum/16925186-post1.html

I believe they have been answered with factual data regarding security of
luggage and concerns regarding transporting luggage on China's HSR.

I will be boarding a train at Shanghai that probably originates there. I will be boarding trains at Nanjing and Suzhou at train stops. So I will be using both scenario A and B. Scenario B is the one I'm most concerned about with the minimal time of the train stop to get on and off.

For scenario B, when the train pulls in for an intermediate stop, are passengers allowed off the trains by those waiting to board before they get on? Or is there 2 way traffic through the doors with people jostling with luggage to squeeze on and off at the same time?

Yes.

Lots of good info here already, here's my 2 bits:

1. Overnight trains only storage is under bunks. Show up early or else you may risk no room. You can store on your bunk too. Top bunks have some space over the door.

2. D and G trains have overhead shelves, really limited to carry-on size. I've seen a few times the female conductors ask people to remove big bags down (I find it funny how they adjust baggage so no straps hang down).

In general, lugging huge bags isn't that big of deal, pretty common for Chinese. But I can assure you it is NOT fun.

先下后上 :)

PSA

http://6.cn/watch/5957461.html

Yes to which part of my question, people getting on and off at the same time or people getting off first then others getting on?

Since we will have a reserved seat, and don't have to rush to get on board to get a seat, if we hold back and let the Chinese push and shove to be the first on/off will we have time to pass through the door of the train after the crowds have moved on/off with only a 2 minute stop? If we stick our leg in the door opening can they close it on us?

You're over thinking this. There is no risk (at all) of the door closing on your toes.

Don't want to spoil the new experiences of your trip.
But here's how easy it is:

Boarding the Chinese Bullet Train - CRH

http://www.youtube.com/watch?v=hAhFPPjXbOQ

Great video, thanks for that. You didn't spoil the surprise for me.

Things I noticed:

1. That platform was almost empty and appeared to be a very small station. I will be using what I expect are busier stations; Shanghai, Nanjing, Suzhou, and Hangzhou. Everyone here on FT has been complaining about how crowded and chaotic Chinese train stations are, how long lines are.

2. It appeared a Chinese lady was sitting in those people's seats. But she did get up and move without being asked.

3. I saw the bag go onto the overhead luggage rack but did not see what the storage closets/areas at the end of the cars look like.

4. How long was that train? How many cars? Is that typical? Wow. That's the longest train I've ever seen anywhere in the world where I have ridden them. Longer than trains in Japan.

5. Are there conductors poking their heads out to be sure everyone has boarded before the doors close and the trains leave? Or is it all automatic? I didn't see anyone working on the platform or train in the video.

Xie xie for the video link.

Definitely overthinking this. If on the platform at an intermediate stop, as the train slows you can read which way the carriages are numbered and can sort of figure about where you need to be and start walking to that point. IME, on the high-speed trains, everybody waiting to get off is by the door when it opens, then once they get off, everybody waiting gets on. It's not the same pushing/shoving deal as the average Chinese subway. You'll have time. The train won't close the doors until the platform conductor surveys the situation on passengers boarding, and blows his whistle, giving the OK to shut the doors and start the train moving.

If you are ever running late and are last-minute onto the platform just before the doors close, just shove the luggage through the closest carriage door and jump in. It will not be fun to work your way with luggage through the aisles back to your own carriage, but it's doable and certainly doesn't rank as a travel disaster. I've been tardy and had to do this a time or two.

Surprisingly with HSR, Chinese pax seem to let people off first. Compare that to 4 years ago in China when it was worse.