SPI Slave Flash programming with two masters question
It should be possible to connect two masters to the same SPI bus provided that


Neither device tries to drive SCK, MOSI, or SS when the other device wants to use it (though SS should be weakly pulled up when idle, and other pins weakly pulled to some defined level).
The devices have some means of staying out of each other's way.


I don't know whether the FTDI bridge expects to be a master or slave; if it expects to be a master but floats its wires except when told by the PC to feed data, and if it has some means of holding the main processor in reset, a direct connection should work out very nicely.  If it expects to be an SPI slave, then the microcontroller firmware will have to talk to the bridge, read data from it, and feed that data to the flash itself.