The purported (and reported) origination point of this train, and the purported destination, according to media reports may be true, or not. Even if true, this train, may have been routed based on pick ups or set outs along that route, to a final terminating yard destination at Chicago.

If it is true, as per the Railway Age report, that this was 178 car train, with half of the units dead in train, then this was definitely a "dog", that would certainly not need the shortest "hotshot" routing you'd probably want for a time sensitive (TOFC/COFC) "hotshot" or even a manifest carload train, loaded and/or blocked for Chicago, or beyond.

Or, just maybe, this train was going to make, or had made set outs and pick ups of some of that carload traffic, at intermediate points, starting from Selkirk, with traffic originating in NY or the Northeast, bound for intermediate points along the route through PA, and on to southern Ohio, before finally terminating in Chicago?

If any of these, including the need mentioned for maintenance windows, are or were, among the reasons for this routing, then none of this routing for a manifest carload make up train, would be "illogical" in any way whatsoever? It would be "illogical" to send this train form Selkirk, via the "water level route" if it had setouts and/or pick ups to make in Pittsburg.