Just in case the title didn't give it away, spoilers for Essex County Express below!

Maybe I'm misreading the resolutions and/or the agenda and act cards, but it seems to me that the worst scenario outcome is to get all the way to the train car then run out of time.

Entering the train car gives the possibility of 1 health or mental trauma, and running out of time on the final agenda card gives you another mental trauma... whereas if you get sucked into the sky-hole before the final agenda card you don't suffer any mental trauma. Is this correct?

In both cases you read the same Resolution passages (assuming that no-one got the train car running).

Yup, sounds right.

I'm partially wondering if this was intentional.

The thing is that agenda 5b says to go to R2 resolution, which really isn't necessary. The card says the investigators are defeated, so adding the "go to Resolution 2" is not needed. It isn't on the other b-sides of the agenda. The consequences would be exactly the same whether or not there was the "-> R2" on the back of 5b.