Both sensors have the same exact spectral channels. So, any difference in flood extent between the two sensors would have to be due to changes in actual flood level between their overpass times (mid-morning for TERRA and early afternoon for Aqua).

Yes, Terra MODIS is in the 10.30 morning pass in the Descending Node, whereas the Aqua MODIS is 1330 afternoon pass in the Ascending Node. For a sun-synchronous satellite, this node difference will result in the the payloads looking at different cross-track areas. Images from Both the satellites will not overlay one on the. Other.