Understanding ARM Cortex, project migration, choosing MCU.

Hi. Lately we have started working on some big project, and we really want to get into the Zero board, working with a strong ARM Cortex chip, but still think mass production (=a cheap,small ARM processor, not like the expensive, big Due MCU)

The thing that really bother me, is the bet I take. For example, if we write an Arduino code to the SAMD21, that uses timers registers, will it be useful to another ARM Cortex ? I guess registers names are completely different..( and what if the samd21 is not going to continue?)

Another thing that I am trying to understand, how is it possible that some ARM STM based boards are working with arduino? http://www.aliexpress.com/item/1pcs-STM32F103C8T6-ARM-STM32-Minimum-System-Development-Board-Module-For-arduino/32478120209.html

Is the whole thing of Arduino is to burn the boot loader to any chip and make it work with Arduino syntax? (don't you must have the board in the list to "connect" the lines of code with the right pins?)

Right now, we really want to work with a new ARM, but we have only 2 options (Due/Zero) , and both have their own problems(Due expensive for mass production, Zero has too many versions and less examples)

Any advice regarding the bet you take selecting an MCU, specifically now with the ARM, that can be migrated, has well established community, and is Arduino based. (Due have it all expect its very bad for mass production of a wearable for example)

(just a thought, should I leave Arduino? if there are out there million ARM processors and I am very limited to only 2, if I choose the Arduino IDE )

Very similar discussion here