The point of the Time Train obviously as ridiculous a concept as it was to clearly show that Doc would be back and that like the refrigerator could build anything he wanted to given the right motivation. I don't see it as a contradiction. Had everything worked out the way Doc originally wanted to I could see him dismantling the car inside of the garage of the mansion if the two of them had come back somehow the conventional way. The Train served for dramatic and creative purposes so that Doc and Marty could have their reunion and Jennifer could ask her lame question about destiny. An obvious question stemming from the appearance would have been where the fuck would Doc have been able to produce the material to construct the time machine? Also by the appearance of his family at least six or seven years have passed (I'm guessing that Jules and Verne are around that age, I can't remember what age they were in the animated series). It was also to probably display Doc as a real life H.G Wells or the Time Machine creator...
Well, it's somewhat reasonable that Doc could build the "refrigerator" out of 19th century materials. A fridge doesn't really require any really complicated electronics to work just a way to compress a gas, something that could've been done with a steam engine. Granted it probably
would take a steam engine and a system the size of a barn to do this but it's possible. The time machine, however, would likely require electronics, computer technology and, most importantly, a way to produce a shit-load of power. Somewhat harder to pull this off in 1885/the 1890s.
So let us talk about the problem Marty and Doc have in Part 3, namely power the DeLorean. Getting gas from the 1885 version of the DeLorean is out of the question. First of all you don't store a car for a long-period of time with gas in it. Second of all tampering with the DeLorean would endanger Doc's plan of getting it to Marty, a plan that had worked. Why risk messing things up?
But, Doc really couldn't find a way to power the DeLorean? Oil and gasoline and automobiles
did exist in 1885. They were very, very, rare to be sure. But they were out there. Doc can make the "Presto-logs" and he can make a fridge but he can't get a hold of a couple gallons of crude oil and find a way to refine it into unleaded gasoline? But they only had a week! You say?
They could've had more time. The situation with Bufford could've easily been resolved. Doc and Marty could've snuck out of town to get out of Dodge, esp after the festival when they know Bufford's weekend schedule, or Doc could've simply tried to make peace with Bufford by offering him the $100 for Bufford's troubles and grievance he had with Doc. Considering the complexity of Doc's shop, his willingness to work on Clara's telescope for free (as well as pay for her horses and buckboard) money is obviously not much of an issue for him. Pay the madman his money; head to a city where you know there may be first-generation cars, and gasoline, available.
Operating the car on the train-tracks is dangerous and stupid. Marty came within
seconds of crashing into a locomotive. (I could also argue that the width of traintracks have changed between turn-of-the-century steam trains and modern-day diesels, and also that the bridge's design is
clearly not one from the 19th century is a of modern design and that over the course of 100 years is entirely likely the bridge would've been destroyed and rebuilt or changed in some small manner.)
Yeah this is all
very petty nitpicking in and otherwise excellent movie but I think all of the plot holes we can find in the second and third movies just shows how bad of an idea it was to write and produce them both
at the same time.