Hello Arduino forum,
learnt a lot here and thanks for all the contribution. 
Wanted to further minify my wearable project and used Adafruit Bluefruit 32u4 Adafruit Feather 32u4 Bluefruit LE with Headers - Assembled : ID 3379 : $31.95 : Adafruit Industries, Unique & fun DIY electronics and kits as a basis for a custom PCB. It has the Atmega 32u4 chip and nRF51822 MDBT40 Raytec module.
The PCBs arrived, assembled them and now I am trying to upload firmware to the 32u4 chip, so I can develop in Arduino IDE (and share with community). Found this link to the BluefruitLE Firmwares. GitHub - adafruit/Adafruit_BluefruitLE_Firmware: Firmware images for Adafruit's Bluefruit LE Modules (Bluefruit LE Friend, etc.)
I assume these are for the nRF51822 module. When trying to upload blespifriend 0.8.0 to atmega32u4 (using dfu-programmer https://dfu-programmer.github.io/), it shows error:
$ sudo dfu-programmer atmega32u4 flash ~/Downloads/Adafruit_BluefruitLE_Firmware-master/0.8.0/blespifriend/blespifriend_s110_xxac_0_8_0_170925_blespifriend.hex --debug 100
Password:
  target: atmega32u4
  chip_id: 0x2ff4
 vendor_id: 0x03eb
  command: flash
   quiet: false
   debug: 100
device_type: AVR
------ command specific below ------
 validate: true
 hex file: ~/Downloads/Adafruit_BluefruitLE_Firmware-master/0.8.0/blespifriend/blespifriend_s110_xxac_0_8_0_170925_blespifriend.hex
intel_hex.c:342: Address offset set to 0x10000.
intel_hex.c:254: Address 0x18000 is outside valid range 0x0 to 0x7FFF.
intel_hex.c:227: Valid address region from 0x0 to 0x7FFF.
WARNING (line 3): 0x18000 address outside valid region,
suppressing additional address error messages.
intel_hex.c:254: Address 0x18001 is outside valid range 0x0 to 0x7FFF.
...
...
...
intel_hex.c:254: Address 0x297EF is outside valid range 0x0 to 0x7FFF.
Total of 0x117F0 bytes in invalid addressed.
commands.c:410: WARNING: File contains 0x117F0 bytes outside target memory.
commands.c:413: There may be data in the user page (offset 0X80800000).
commands.c:414: Inspect the hex file or try flash-user.
WARNING: 0x117F0 bytes are outside target memory,
and will not be written.
atmel.c:1153: atmel_flash( 0x7ffeef6b6920, 0x7ffeef6b6810, false, false )
intel_hex.c:673: intel_flash_prep_buffer( 0x7ffeef6b6810 )
atmel.c:1193: Flash available from 0x0 to 0x6FFF (64kB p. 0 to 0), 0x7000 bytes.
atmel.c:1197: Data start @ 0xFFFFFFFF: 64kB p 65535; 128B p 0x1FFFFFF + 0x7F offset.
atmel.c:1201: Data end @ 0x0: 64kB p 0; 128B p 0x0 + 0x0 offset.
atmel.c:1206: Totals: 0x2 bytes, 4261412866 128B pages, 4294901762 64kB byte pages.
atmel.c:1216: ERROR: No valid data to flash.
Hex file error, use debug for more info.
commands.c:514: Error writing memory data. (err -1)
Current status notes:
- The atmega32u4 is recognised by a computer when connected via USB.
- dfu-programmer recognizes atmega32u4 chip connected.
- The BLE module does not appear (might be invisible - not sure).
Three questions:
(1) I assume the atmega32u4 has an DFU bootloader that allows USB programming from factory, as per avr - Custom Atmega32u4 board first boot - Electrical Engineering Stack Exchange. If I burn an Arduino bootloader on it, will it replace this DFU bootloader and subsequently work in Arduino IDE? Or the DFU bootloader will still be there and using dfu-programmer I will only upload an Arduino firmware as mentioned here: https://www.arduino.cc/en/Hacking/DFUProgramming8U2 For a circuit to work with Arduino, do I need Arduino firmware or Arduino bootloader?
(2) I found firmwares for other Arduinos using 32u4 such as Leonardo. Can this be used in my case or do you know a source for the atmega32u4 firmware in Adafruit Bluefruit 32u4?
(3) How would you proceed to upload the firmware to nRF51822, if I cannot see the module? What could be a possible problem other than wrong connections?
I am a complete beginner regarding bootloaders/custom PCBs, trying to learn how it all works.
//posted same question to adafruit forum, will share insights.