For the Imperial Taxation Department, this is no problem. Their tax collection is sufficient; what is collected is the tax currency itself, which means other places compensate for this tax, resulting in no loss. In fact, many businesses are proactively initiated by the tax department.
Profit is profit, no matter who earns it.
It's not just them profiting; those trade associations and caravans from Holy Terra have backgrounds too. Everyone has to make money!
The profit from mere price differences is enough to eat well!
This is only one factor, namely that tax valuation is lower than market pricing.