That's one expensive way to build a railroad. If they went to that much effort and expense, it should have been dead flat across Indiana. Conversely, it should have had a very low cost to operate.
No railroad is 'dead' flat for any real distance. The New York and Chicago Air Line was going to attempt this (nearly flat ROW), and its efforts petered out around Westville, IN because of the cost.
The upper midwest is very flat compared to most areas. We can thank the last ice age for that. However, there are large "escarpments" that surround the Great Lakes that mark the former shore lines of these lakes following the last ice age. So, while Indiana is generally flat, its not without its gentle grades. The nice thing about these grades is how gentle they are. It lends itself to long fills and cuts to keep a gentle profile for the railroad.
These fills are expensive and when building a railroad, you just want to get it done. You can come back later and build it to better standards. Just look at the transcontinental railroad in the late 1860's. Track looks terrible as they initially laid it. They came back later and added ballast, etc.
Long tressels weren't uncommon back then. The railroads would come back in and fill it in later, after traffic had started. Garrett, IN was originally built on tressels over the swamp that underlays the town. Supposedly, the B&O came in and dumped coal trains for fill and whatever garbage they had laying around. To this day, if you dig a hole in Garrett, you'll find cinders, coal, and garbage from the construction. I believe the first Horse Shoe Curve near Altoona was a large tressel that was later filled in across the valley.
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