[2.0.x] Clean up ST7565, dual endstops homing

* Misc fixes and improvements

- Get rid of most critical sections on the Serial port drivers for AVR and DUE. Proper usage of FIFOs should allow interrupts to stay enabled without harm to queuing and dequeuing.
  Also, with 8-bit indices (for AVR) and up to 32-bit indices (for ARM), there is no need to protect reads and writes to those indices.
- Simplify the XON/XOFF logic quite a bit. Much cleaner now (both for AVR and ARM)
- Prevent a race condition (edge case) that could happen when estimating the proper value for the stepper timer (by reading it) and writing the calculated value for the time to the next ISR by disabling interrupts in those critical and small sections of the code - The problem could lead to lost steps.
- Fix dual endstops not properly homing bug (maybe).

* Set position immediately when possible

[2.0.x] Fix / improve junction deviation

- Respect axis max acceleration limits instead of forcing a fixed acceleration value.
- The `junction_unit_vec` ensures proper handling of entry and exit speeds even when the axes involved have different limits.

Don't build and link with different flags, the binary may not work.

Co-Authored-By: zarthcode <anthony.clay@zarthcode.com>

Fix #10896

[2.0.x] Rename and document some configuration options

[2.0.x] LPC1768 upload_extra_script.py fix (wrong type of exit method)

Co-Authored-By: ejtagle <ejtagle@hotmail.com>