The 5V pin on your board is an in and out pin. As an input, it will accept a voltage range between 4.8V and 5.2V. Please do not connect any power source over 5.2V to the 5V pin and please do not connect your battery to the 5V pin. It is for a 5V power source only.
When USB power is connected, you will get approximately 4.9V out of the 5V pin. The voltage drop is due to the reverse USB power diode that allows the USB and 5V pin to be power inputs at the same time, and prevents back feeding power into the USB.
The use case for having both connected is when you want to power your board from the 5V pin from an external 5V power source, but you also want to connect the USB to flash the board, or to get serial output.
If your board is being powered by any 5V source (USB or 5V pin) and a battery is connected to your board via the VBAT pin or connector, the battery will go into charge mode and the board will be powered via the 5V source.