I am not sure I understood the questions correctly.
Can you please elaborate a bit on the questions?
I am assuming the first question is about how to creat one bin file from all the binaries(filesystem.bin, DCT.elf, <application>.stripped.elf) without including the bootloader.bin file.
You can use objcopy to combine the individual binaries. The individual files can be located in build folder. If snip.scan-CYW943907AEVAL1F is build, the corresponding directory will be 43xxx_Wi-Fi/build/snip.scan_CYW943907AEVAL1F