Secure signals on boot time to prevent unwanted operations
During the boot sequence the I/O-pins are usualy pulled up with high impedance so they can not damage other parts. For the registers and the memory of the FPGA you can define the initialization with the constraints editor.

If you build the PCB yourself it's your job (with the help of the data sheets) to provide the appropriate reset signals (perhaps sequential) to the various parts. Eventually you will need also some pull-up or pull-down resistors or additional logic. You also have the possibility to control the startup of other parts/modules with your FPGA.