The only downside to locating the thermowell downstream is that the response time of the flow meter is usually much faster than that of the temperature measurement.
This means that if temperature delayed response is critical it is better to install upstream but make sure to be outside the meter required upstream flow conditioning. This is most likely to be critical where a step change might be expected in flow and/or temperature.
Hence if the temperature sensor responds slower, the delay is partially offset by the flow delay i.e. the time taken by that portion of the fluid to flow to the meter.
However, as ever, it is always best to follow the industry/international standards or manufacturer's recommendations about the location of all instruments where appropriate.