The flash should be initialized if the following is true.
# if (!defined(ALT_EXCLUDE_CFI_FLASH) && ((!defined(ALT_USE_SMALL_DRIVERS) && !defined(ALT_SIM_OPTIMIZE)) || defined(ALT_USE_CFI_FLASH)))
The easy way to ensure this is to just define ALT_USE_CFI_FLASH. In the BSP Properties under NIOS II BSP Properties add "-DALT_USE_CFI_FLASH" (without quotes) to Defined Symbols.
I have problems when I have two BSPs for the same processor, but I am sure that is different than your situation.
There is a global device list that should be filled out when alt_main() executes. Watch the global alt_flash_dev_list as you step through alt_main().
Since you are using three processors and I will be in the future, I have a question for you. I have seen some people saying that they cannot debug three processors at once, have you experienced this problem?