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Most of my trains will be 3 cars, but I prefer longer trains to more trains when its called for. I'm aware my intersection exits must be a full 6 cars, but it seems that there would be an advantage to setting everything else up as 3 train cars.

Example of what I mean

With 6-car exit blocks, I think uncongested traffic will generally maintain that 6-car distance at all times, because the leading train's got that much of head start on accelerating ahead of the following one. Any train that gets closer than 6 cars will have to brake to reestablish that distance for the next intersection exit, see?

So 3-car intermediate blocks would only make a difference when there's congestion, you'd just be packing more trains into a congested leg, I don't see how that helps get anything through that next 6-car-exit-block-throttled intersection any faster.

...hunh. I'm pretty sure this simple-looking setup allows deadlock-free 3-car intervals even in the face of 6-car trains by providing a bypass failsafe for 6-car trains that hit congestion on the way out: Copy blueprint

The red signal at the top center, the bypass entry signal, is wired close-if red<2, i.e. it's open if and only if a train is actually occupying both 3-car straight blocks below it. So there's a train in the chain-guarded merge exit to the right, so no other train's got the merge reserved. There are at most two trains to consider here.

The one-train case is trivial, it's in both straight blocks and either another train will arrive after it leaves the merge exit (which will produce the two-train case) or it won't (closing the bypass). Only the two-train case is interesting: the leading train's in the lower bypass block, the following train's in the merge-exit 3-car.

Now, here's the trick: the bypass (upper) segment's not long enough for a 3-car train, not even including the rejoin curve, but the bypass plus merge exit pair is long enough for 6, so

• any train taking the bypass will occupy both bypass and merge exit
• because of the signal wiring no train will ever take the bypass unless congestion has caused a previous, leading train to brake, and
• since the bypass exit is guarded by a chain signal, any train leaving the bypass block is guaranteed to be able to enter the following rejoin-exit 3-car block too
• but: if a six-car train leaves the bypass block and can't continue past the rejoin exit, its back three cars will still overflow the bypass block and leave it occupying the merge exit:

  

  snap@T342368=5264x976-46.75-24.25,z2.jpg (146.6 KiB) Viewed 1133 times

I think that's the worst case, a six-car train forced into the bypass and unable to clear it on exit, so, to answer your question, no, unless I'm missing something you can use six-car trains on a 3-car-blocked rail, and this bypass even lets you maintain deadlock-free 3-car spacing through intersections with 6-car trains.