Working with Arduino Due in native way

Hi all, and first of all sorry for noob question.

I have some years of experience with PIC16, PIC18 and STM32 arm based controllers. Recently a potential customer has asked me to do a project using Arduino Due boards (because he beleives due boards are pretty stable, I believe that of course).

What I want to know, is there a factory installed bootloader on Due controllers? Can I program it in its native way using atmel studio, without meddling of any arduino related bootloaders? I mean can I program them like I bought bunch of new chips from a supplier?

Thanks!

he beleives due boards are pretty stable

There is some question as to whether the Due is still a "current product."
https://groups.google.com/a/arduino.cc/forum/#!topic/developers/HEKecd0qhS4
(still, there are third parties producing Due compatible boards.)

is there a factory installed bootloader on Due controllers? Can I program it in its native way using atmel studio, without meddling of any arduino related bootloaders?

The SAM3X cpus have a built-in (ROM) bootloader (SAM-BA) that will bootloader from either USB or Serial. In fact, I think that the Arduino IDE uses the standard Atmel utility for "uploading" to the Due (with some added features for auto-reset?) Real Dues have a JTAG connector for "real debugging", but it looks like this is not present on all the clones (I can't find a JTAG connection on my "ITeadDuino Due", for example.)