IIRC (i.e. not necessarily correctly) canals were exempt.
Nevertheless I'm fairly sure that the prohibition had to further commerce somewhere in it.
But the Govmint figured out a way around this provision during the war very quickly I've seen quoted that in OTL a Senator (Representative?) bitterly complained that "national security" allowed the Government to fund railways and basically anything it wanted.
Hence a post war transcontinental RR would receive Federal funding and be built to aid defence.
In
this recent thread (in which I also demonstrate quite clearly that I
don't actually subscribe to the view that
@Urabrask Revealed lampooned earlier), I argued that there would be very little logic in post-war revanchism from either side. Precisely because economic considerations would win out, there would soon be an "era of good feelings" (or if not good, then at least okay). This means that the excuse of using "emergency powers", "threat of war" or "vital defence" as a political excuse would evaporate.
The CS Constitution aimed to allow for (con)federal investment into... well,
anything, really... only if it was absolutely critical for defence. So rather than an exception for canals, there was an exception that would (under reasonable peace-time conditions) allow the central government to build docks for the navy, for instance. But that would be about the limit.
We have to consider that the slavocrats were, by the nature of their economic set-up,
always in debt. This is one reason why they struturally opposed all forms of direct taxation. And they'd be making the decisions in the CSA. So the idea of the CSA building a trans-continental railroad with (con)federal money can safely be dismissed. As soon as the war is over, the war measures (at least in a fiscal sense!) will be abolished
immediately. Doing so is not just politically preferable to the ruling elite,
it is a prerequisite for their economic survival. They only ever allowed (unprecedentedly) 'big government' during the war because
that was perceived as the more pressing existential crisis.
But once that crisis is resolved? Right back to the old stand-by of "low tariffs, no other taxation ever, certainly no direct taxation, and the government should be very small... in fact, it should
basically just be a police force that
we control, thank you very much..."
BTW - the CSA Founding Fathers (and their political mentors) had more than a 50% share in the running of the USA since the country was established - and they suddenly go all stupid?
They were always opposed to centralism and to higher taxes.
The great mentor of the men in question was Calhoun. Hey, what was
he (in)famous for again? What's that? "Nullification Crisis"? Ah, yes! See there, the basis of the Southern Democratic political platform, clearly laid out.
They weren't stupid, they just had specific vested interests. As I mentioned, they were always in debt. Only under a low taxation regime could the plantations survive. Direct taxation would be crippling. This leaves indirect taxation, meaning tariffs. Which is nice, but those need to be low, too, because a plantation economy relies on export, so it only thrives by the virtue of a free trade regime...
You can see the obvious conclusions, I'm sure.
You are thinking about the interests of a CSA that wants the best posible future for itself, and does the sensible thing when viewed from a long-term perspective. Because of this, you reject the idea that the CSA
must become a backwards second-tier nation. Conversely,
I am pointing out that the CSA was actually 100% under the control of an elite that served its
own interests, which happened to be fully at odds with the long-term goal of effectively developing the country.
This means that
in practice, the CSA was indeed doomed to become a backwards second-tier nation. An elite directly opposed to all the steps that are necessary for modernisation, paired with the presence of an ethnically distinct permanent underclass, is not a recipe for success. More like the opposite.
Again: South Africa meets Brazil. That's your CSA.