I can sort of see that argument, though I do think this is a case of perfect being the enemy of complete.
I guess the "proof of concept" was already made, but I think this is still just pioneer technology in the Duke's eyes. The train working smoothly for the next year or so would already be enough to call it a resounding success in my book.
Things like wear and tear of parts, obstacles to future expansion, and sabotage are things that they can worry about and improve upon as it comes up.
Like you said, fantasy materials and enchantments can mitigate it. But more important than those fantasy engineering shortcuts is Miyabi himself. If there really were any need to expand the rail network and rework the current ramp system, then Miyabi can dismantle and remake the entire site within the day as long as someone can figure out a blueprint. He can rapidly create replacement/spare parts too.
And that's only assuming there's any major urgency to the matter. I imagine it could be turned into an economic and social boon for Crafters and craftsmen, since the train remains productive enough in concept to be worth any maintenance costs if the Duke's estimate of 10s of millions is accurate.
Also, I'm not sure if you're just referencing something different from what I can imagine, but being down for maintenance feels like it would only become an issue if people become dependent on it to the point of lifestyle changes. This train as it's currently designed crosses 2 weeks' worth of travel in half a day, so maintenance can take a full 10 days and it would still be better sitting around waiting for maintenance to finish than not having the train at all.