Flare fittings are a pain in the butt in many respects. They are expensive to purchase as a regular consumer and require attention to detail in craftsmanship when creating flares from straight pipe. I use some of these fittings in automotive applications such as fuel lines between pump and filter and fuel rail to filter. They are most often found in brake line replacements to eliminate some of the squishiness between the time when the pedal is depressed and the hydraulic system reaches sufficient compression to begin activating.
The amount of overlap depends on the engine, but most modern fuel injected high performance internal combusion engines have some valve overlap. While the intake valve is starting to open, the exhaust valve is starting to close. During this time there can be a back flow of air/exhaust in the direction of the fuel injector and intake manifold. This effect is stronger under high vacuum conditions (low absolute pressure). It is important to wait for this back flow to reverse before firing the injector. Once the exhaust valve is open, the velocity and flow of air will have increased as the exhaust gases have completely turned around and begun to escape through the exhaust port and out of the exhaust manifold. The optimal time to fire the injector is during this period, but as engine speed increases the injection must begin earlier to fully complete to avoid flowing fuel straight through the combustion chamber and right out of the exhaust port.