Here's my counter argument for why it's not Skaven, or at least not directly: there's literally no point in sourcing all the materials from Imperial foundries, because the only people who can tell are the Gold college, and the only reason they'd include that detail in a dwarven hit requires way too much double think and additional explanation for something happening half the Karaz Ankor away from the only golden wizards they let live within ten miles of them.
In addition, those materials are sourced in a line straight from Marienburg to the location. No identifying materials mean that Marienburg is the default suspect, but they've been sourced exactly how I'd expect an actual operative from Marienburg to source them anyways.
And you don't need to be a superspy to pick up a shady barrel of the good black powder, just lucky. Remember, it's entirely possible this wasn't meant to sink the boat at all, which drastically opens up the potential acceptability of an attempt's effectiveness.