Can confirm they've started chipping toner carts now :/. I have two Brother printers, one that takes TN-450s (no chip, can be reset via button sequence) and one that takes TN-760s (chip, no button sequence reset to say the cartridge is full). Both can be set to 'continue printing' when the cartridge is 'empty', though*.
* Sometimes it "forgets" this setting, unsure the conditions to trigger that, but I imagine the retention sloppiness of this setting versus all the other ones it remembers (admin password, etc) is not an accident.
I have had a Brother MFC-L3750CDW for 3.5 years, and have printed over 5000 pages.
Even though I always use third party toners, I haven't seen that color registration issue.
Just now, I just went to the printer and let it do the 'calibration' and 'registration' steps. Then I printed a test image from the internet. None of the colours are offset.