That output is from the actual firmware which I think doesn't know or care about bootloader. Can't remember if the boards with a bootloader print anything else during boot...
Haven't had any bootloader-less boards so can't be sure, but the way to check if there is a bootloader actually is to try to upload the firmware using the USB connection; it it uploads, you have bootloader. If not, no bootloader. And if no bootloader, you need the thingamajig USBtinyISP to program the board.

Alternative for modifying the firmware is to use gcode-commands to change settings using the USB-connection. Pronterface is good for this, as is Octoprint. Haven't used S3D or other USB interfaces. Octoprint even supports Marlin EEPROM editing with a plugin. If the board has EEPROM enabled, you should be able to save the settings with M500-command. If not, you need to issue the commands every time printer is started.
You can change axis steps with M92-command https://www.reprap.org/wiki/G-code#M...steps_per_unit. From your firmware output it seems that current settings are X78.74, Y78.74m Z2560 and E105. So modify the M92 line for correct steps, they should be active immediately.