1) No, it only affects the hurry options in the city screen, i.e. from Despotism and Public Welfare. Great Engineers always grant the same amount of hammers regardless of the building.
2) Buildings for which no building cost modifier is applied use the default modifier (100), you can simply add a tag to give them a different value. I don't know what a negative modifier would do but probably nothing great. 100 means you pay 100% of the price, 0% would make hurrying free (probably capped at 1 gold and 1 pop) etc. You are always affecting pop hurry and gold hurry equally. It seems you want to buff Public Welfare, for which I recommend looking into Assets/XML/GameInfo/CIV4HurryInfos.xml, e.g.:
Code:
<HurryInfo>
<Type>HURRY_GOLD_BUILDINGS</Type>
<Description>TXT_KEY_HURRY_GOLD_BUILDINGS</Description>
<iGoldPerProduction>3</iGoldPerProduction>
<iProductionPerPopulation>0</iProductionPerPopulation>
<bAnger>0</bAnger>
<bUnits>0</bUnits>
<bBuildings>1</bBuildings>
<Button>Art/Interface/MainScreen/CityScreen/hurry_commerce.dds</Button>
</HurryInfo>
You can set the gold cost for each hammer for each different method of hurrying here.