The key tutorial is the same as in the earlier version. It does occasionally instruct you to accelerate right before a terminus buffer stop so there's still room for improvement! For a funny example of this, see GrayStillPlays' Let's play video (he's playing version 1.0). The reason why the tutorial suggests fiddling with the brake at stations is because it's trying to match 15 inches of vacuum which is the standard for keeping the train still. The vacuum gauge works with some delay, especially in longer trains, which is why you see the needle dropping occasionally below 15in even though the brake valve is lapped. You're right though, it's confusing for a beginner and I'm still going to fine tune it in some of the future updates!
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It's super-useful to have that guide - esp as the game has the 'score' aspect for best driving practices!!
It also maybe distracts people a BIT from learning trains properly - I had to force myself to turn-it-off - I believe remapping is possible so maybe I need to remap to TS settings to avoid having to think so hard? :)