You can only set these segments to 'flash' if you actually burn them to flash. The normal download step tries to simply write the contents of the segments as if the destination was RAM.
If you are planning to burn your program to flash and run out of flash you need to run FlashProgrammer first, then you can run the program. I'm not sure what to suggest for the download portion, you could try letting it download and see if the verify works since the correct stuff should be in flash at that point.
One thing to be aware of is that you won't be able to run out of a flash chip and write data to it from the same program, at least not in general. I fell into that trap before.
If you are planning to burn your program to flash and run out of SRAM you don't have to do anything, just run flash programmer, set your reset address to flash and you're good to go.
