TL;DR: I don't see I-69, if completed, doing much to damage railroads in the same general corridor. The railroads are already doing it to themselves even without most of the highway. They may succeed in making themselves Interstate-proof by driving away the traffic that can feasibly shift to anything else; most of them are already well into that process. It's not a growing industry, despite some highish stock valuations - those stock values are based on the continuous PROFIT (not traffic or revenue) improvement demanded, and delivered, by PSR and its derivatives.

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The purpose of all of the Interstate system, original or extended, is to enhance trucking. Ike hated railroads, and his Interstate System invention was intended to eliminate the dominance of railroads in the goods-hauling business. I'd say he succeeded. Passenger trip viability and the growth of auto-oriented suburbs are intended byproducts of that, but not a fundamental purpose.

So yes, completion of I-69, or even a significant usable portion of it, would affect all sub-parallel railroads in a similar market. But not by much.

Containers (as opposed to semi-trailers) are not viable for long-distance trucking because of the inefficiency of the trailer frames needed to haul them. They *are* more efficient for long-distance shipments than trucking. So if the shippers continue to use containers for runs like Mexico-Canada with incidental drops in the US, the effect of an I-69 would relatively modest absent a large-scale shift to trucks for the whole trip (you've heard of a driver shortage - because nobody wants to increase their costs by paying a living wage?). Also, railroads in general in the US are interested mainly in large block moves and unit bulk trains; they've abandoned the non-bulk, non-container market (i.e. loose-car railroading) to trucks already. So the effect of the freeway would be less because railroads are intentionally locking themselves into a market niche that's resistant to competition; they're not really looking for traffic growth. They're really just looking to make more money per year per ton hauled of what they've got now.

It's called improve-the-margin so bigger dividends can be paid to the investors. You improve the margin not by hauling more, competing for traffic with the trucks, but by hauling less, at lower cost (keep cutting that operating ratio!), and raising the rates regularly to more than make up for the lower traffic.