Sample Wares Intrigue Card Disambiguation
This has been answered by designer Rodney Thompson on BGG here

You gain the primary benefit of the action, not the owner's benefit. The part about &quot;as if you controlled&quot; the building is simply there to dispel any questions about where the owner benefit goes. Just like when you assign an agent to a building you control, you gain only the primary benefit, not the secondary benefit.
However! If you are playing with the Undermountain expansion and have completed the plot quest Impersonate Tax Collector, you would gain both the primary benefit and the owner benefit.