From my understanding, nothing has really changed. The part of the reg you didn't copy into here is:
(e) Logging pilot-in-command flight time. (1) A sport, recreational, private, commercial, or airline transport pilot may log pilot in command flight time for flights-
(i) When the pilot is the sole manipulator of the controls of an aircraft for which the pilot is rated, or has sport pilot privileges for that category and class of aircraft, if the aircraft class rating is appropriate;"
On a checkout flight, you have a pilot certificate and are rated in the appropriate category and class of aircraft. On 99.9% of training flights, you are the sole manipulator of the controls during the flight. This has always been the wording that allows you to log PIC during training.
The part you quoted, to me it seems like a way of letting those training on higher performance aircraft to log PIC time. The stipulation to have at least a commercial is what makes me think that. I could be completely off base on that assumption though. But personally, I don't see why that was added when the above part of the reg has always been there.