Hi there,
Sure , check out the Creating a standalone bin file. demo
I don’t know about what yours comes with , So send them an E-mail and ask?
Yes Flashing bootloader is part of if you want it as part of the process.
You may not need it for production. just the Softdevice and APP
Reading the chip you see the different partions.
Note the NAMES in each file that’s combined, just like when you press upload in arduino IDE.
There’s tons of video’s about the BOOT loaders for allot of MCU’s adafruit has a series also, as well as NRF52.
HTH
GL 
PJ