Huh, that is a very interesting divergence from the original Star Wars Plot.
After all, as original defined in movie and legends, the issue of taxation was the question of whether these routes should be taxed at all. The Federation objected, and it's blockade of Naboo was a matter of strongmanship, to force the Republic to fold and withdraw the taxation bill.
Having the bureaucracy and the Trade Federation on the same side is a suprising divergence, that redraws the lines of power. Because without a bad relationship between Republic State and the Trade Federation, the latter does not have as much motivation to support the Confederacy.