At some point it was necessary to add a 91ft wooden ramp to the West end.
Railroad bridge unlikely. The steam engines were prone to leaving hot cinders and were hard on even open wooden structures. Witness the bridge at Gosport where the railroad ran past one end. That end of the covered bridge caught fire and was rebuilt as an iron truss resulting in a three span bridge with two wooden covered spans and one iron span.
There were covered railroad bridges, but I don't think any of them survived very long.
Of course the railroad idea is pure speculation, but given the crazy height of this bridge it is a possibility. I doubt there would be any relation between this and Old Nellie however. I wonder if it might have been built for a planned line that was never completed, to which the county later turned into a road. It's possible as well that the Kennedy's felt the taller trusses, with those massive arches, would be better for 2 long spans across the river.
I have visited the site from the east side and didn't see evidence of no trespassing, but... West side looks to be fishing shacks and whatnot.
Finally, the Old River Covered Bridge has been added! Sure was massive for a wooden covered bridge. About it possibly once being for railroad, I wonder if 18 feet wide was enough room for two tracks. I think this and Old Nellie Railroad bridge were built about the same time, and they weren't far apart. So I wouldnt know. Since this bridge was never replaced, I wonder if either side is private property now? If not, then this would be the place to build a modern covered bridge! Build one here and not in place of a historic metal truss that was just demolished!
Not saying it was ever used as a railroad bridge, but it might have originally been designed for a line that never came to fruition. We did indeed have some covered railroad bridges in the state, and you are correct in that they didn't tend to last for long. The spans were normally wet down before, and a spotter was usually employed to make sure there were no live ashes on the bridge after the train passed.
A fire at the Gosport Bridge in the mid-1880's is one of several different stories as to why the West span was replaced, I've yet to see documentation yet to prove one of them.