Most of the shops I visit to purchase my supplies dispense an alcohol-based hand-sanitiser at the point of entry and have a person stationed there to check customers’ body temperature with a contactless thermal gun. They used to point the gun at the forehead but of late many of them have started aiming it at the other side of the palm, to be held outstretched. I don’t know if this is okay or not – but I doubt it’s okay to point the thermal gun at the hand just after you’ve doused it in sanitiser.
Alcohol’s two properties of interest in this context are that it’s a disinfectant and that it’s volatile. After you’ve applied it, your hand feels cooler because each droplet of the alcohol absorbs a tiny bit of heat from your body and evaporates. This is also why you and others around you can smell the sanitiser’s fragrance spreading: the alcohol molecules are airborne and floating about, no longer localised to a smaller area.
The difference between a liquid and a gas is that molecules in the liquid are held together by bonds between hydrogen atoms and certain electron-rich atoms – for example, oxygen in the case of water. These bonds can be broken by heat. Volatile liquids have fewer of these bonds, so they need less heat to transition from the liquid to the gaseous phases. These liquids have relatively lower boiling points (than water in the same conditions) for the same reason – 78.3º C and 82.5º C for ethyl alcohol and isopropyl alcohol respectively.
If at this point the thermal gun is pointed at the hand, I’m not sure it would still be able to pick up a fever – especially a milder one close to the threshold of 99º F. The cooling effect is transient but the sanitisation and the temperature check happen within seconds of each other. I’m also not sure how effective thermal guns have been in general at screening people with fever at various checkpoints. But if they are, pointing them at the forehead or at the hand but before using the sanitiser could easily preclude one issue.