Partially.

Holdings now have separate values for income and "local defense budget" (LDB).
Your income is, obviously, how much they put into your bank.
The LDB is value subtracted from the upkeep cost of defense buildings.
If the cost plus LDB > 0 then the difference is subtracted from income.
If the cost plus LDB < 0 then income isn't affected. This is the important part.

In the old system that negative cost would go into income but now it only goes into the LDB and any surplus gets discarded.

So income buildings no longer boost income, but they still can offset building u[keep costs if you add them into the structure. If this decreases the upkeep to 0 or less then that building will no longer cost anything to maintain, but you won't make any profit from it.

If a modder wants to fix this then I suspect they'll need to find whatever line cuts off surplus from going the income and disabling it.

After the update after Diplomacy which was a bug fix and other stuff, adding a industrial building now does that. But also removes the Unrest, as in, my buildings remove 20 unrest from a city. If I slap on a tree farm from Cataclysm, it gets removed and now I have a city in revolt.