Miyabi is being really silly with this project. He doesn't even know how to build the engine for the locomotive and he's aiming for a train? He should be working on a car instead; far less horsepower needed and can travel on the existing road infrastructure. It will also fulfil the intended purpose of enabling two adventurers to travel more quickly over the 600 km distance.
Beyond the myriad of issues that come with such a project (permission to build, maintenance cost, etc), it seems to me that it will attract attention to his skills and he may be "asked" to keep working on such projects to link up other cities because he'll be able to do it in a fraction of the cost and time that it would take otherwise. Changing the travel time from two weeks to 12 hours is pretty transformative for the economy and the military after all, so there's no way the nobility and royalty won't ask him to contribute further. Then again, there is apparently a guild of infrastructure and production that manages such matters, so he'll probably be shielded of such work by the guild taking on the requests to build that type of infrastructure.
MC already created a system based on wind magic as mentioned in the chapter, though on a much smaller scale. And he doesn't really need to create a full-on locomotive engine. What he need to do is create a engine with a strong body and good breaking system. As for propulsion system, the answer is magic, aka., no need for complex machinery like steam engine or electric engine, but rather need for Enchantment based powering system, which MC can already create quite easily.
He can't really create full-size prototype without getting permission on construction for the project, since he would need a lot of materials and for that he would need help to gather.
And he already mentioned why he didn't consider "above-ground" solution, as using car wouldn't really help by much, since they would be taking the same route they used to travel by the horse-cart (which isn't a simple route).
Even with car's speed, he would only be able to reduce travel time from around 2 weeks to around 4-6 days on existing route (unless he creates new roads which would create more hassle). Plus he would have to think about road-traction, anti-snow & anti-monster measurements as well.
And this isn't MC's goal with this project, as he wants Liz to be able to do Adventurer work on her weekends so that she doesn't lose her license while attends academy on weekdays. And a travel time of more than a 24 hours is going to make his goal useless.
For a roughly 600 km distance, to hit the under 12 hours of travel time target, MC would need to create an engine with high capacity to go 50+km/h on average. This kind-off speed isn't possible for a car above ground, unless the road is perfectly pitched and there are no slowing down issues (like monsters or snow storm, etc).
As for later on, yeah with this project many people would learn about MC's capabilities. But they wouldn't really need to be stuck to just MC for his help. From what i understand, except MC's huge magical capacity, his abilities with crafting is something which could be learned by other Crafters, and all they need is good training and a open mind for imagination.
Not to forget, the Duke already knows and keeping an eye on MC, so it's not like hiding his abilities is going to profit MC in anyway. Making his usefulness known is another way to keep himself alive, as some might consider him as a dangerous individual.