A number of the things you list also have analogs in Ozu's work. Ozu has a wide array of train scenes of almost every sort.
But in all of the films in the 4 Shochiku boxsets that I've seen, there are no train scenes similar to the ones that I described. I've never seen a shot of a train crossing a small bridge in the countryside, with a body of water in the foreground. In "Summer at Grandpa's", the body of water is a stream; in "Cafe Lumiere", the body of water is a pond. In both films, the trains travel from the left to the right side of the screen. I think a landscape like this (a small bridge over a stream in the farm/countryside) is rare in Japan.
It's the same case with the camera looking ahead of the train. I've never seen such a shot in any of Ozu's films. Ozu's films have train scenes with the camera looking in the forward direction, but the camera is never mounted inside a train (in the front) and looks ahead. (In "Late Spring", for example, the camera looks in the forward direction, but it's mounted to the side of the train).
He also has a variety of tombstone scenes (can't recall the trees in these, though).
Of course you can't recall tombstone scenes with trees in Ozu's films. There aren't any. Yes, Ozu's films has tombstone scenes ("Floating Weeds", "End of Summer", "Tokyo Story") but it's the shot of a big tree in a farmland that we're talking about here. And the tombstones under the tree or the religious shrine under the tree is just another link between "Cafe Lumiere" and HHH's previous work.
I don't know if I should mention this, because it weakens the point that I'm trying to make. The only "big-tree" scene in an Ozu film that I can think of is in
"Story of Floating Weeds" where the girl was waiting to seduce the boy. There are some kind of small flags under the tree.
The white blouse and dark skirt occurs frequently in Ozu's films -- even if this is not often seen on the streets of Tokyo today.
I'm not talking about "dark skirt". I'm talking about "black skirt". There is a difference. "Dark" could be "navy blue" which is very popular in Japan or grey. It's the black skirt and plain white blouse combination that is rare in Japan. I've been to Japan's big cities, small cities, even a fishing village like the one in "Maboroshi". I once spent the whole afternoon in Shibuya just watching people and never saw people wearing that attire. And Shibuya is a place that is crowded with people, especially at the big intersection that is similar to the one at Time Square in NYC.
Maybe you should try sitting closer to your TV screen (like I do). Then you'd have no problem seeing the lovely actress's face.
Or buy a bigger TV

Except with a split second in one scene, did you have a good frontal view of the actress's face in this film? HHH always filmed her from the back or the side (of her face), but not the front. Look at the screen captures posted at DVDBeaver, it's the side of her face that was filmed, not the front.
And by the way, here are a couple of things that HHH has said about "Cafe Lumiere" (not these exact words, of course). I can't remember where I've read or heard about them, maybe in my dreams:
1. That he tried to imagine how Ozu would shoot a film in modern-day Japan when he was shooting "Cafe Lumiere". (Yeah, right, to think that the Master would shoot a film in modern-day Japan to look and feel like a HHH film? Never!)
2. That he was making a "Japanese film". Hahaha. I don't think so.
I can imagine a scenario in which, after watching a pre-release private screening of "Cafe Lumiere", the Shochiku executives, with a dazed and confused look on their faces, huddled in a corner of the theater and asked each other this question: "what was that?"
