14 CFR 61.51(e)(2) does not limit an ATP to logging pilot in command time in a specific manner. Rather, it provides a means by which an ATP may log time as PIC when not flyign the airplane. This is differentiated from the basic privilege of sole manipulator spelled out in 61.51(e)(1). It extends more lattitude to the ATP; it doesn't restrict the ATP.
As A Squared pointed out, there is a big difference between logging pilot in command time, and acting as PIC. One may be acting as PIC, but be unable to log PIC time under certain rules. One may log PIC time while not the designated or acting PIC of a given flight. In some cases, two pilots may log PIC at the same time.
Under 121.437(b), both pilots do not need to posess an ATP certificate. Only the pilot in command needs to posess an ATP certificate. The SIC may hold a commercial certificate, and is eligible (if qualified in the airplane according to category, class, and type) to log time as pilot in command when acting as sole manipulator of the controls, in accordance with 61.51(e)(1)(i).
The passage already discussed, regarding the ATP certificate, permits pilot in command designated by the certificate holder (who is required to hold an ATP certificate) to log the flight time as PIC regardless of who is flying. It doesn't restrict the designated PIC/ATP, but enpowers the ATP to log the time even though not flying the airplane. It speaks to his experience, authority, and responsibility in acting as pilot in command.
121.385(c) provides that the certificate holder shall designate the pilot in command. The pilot in command shall remain the pilot in command for the duration of the flight (unlike operations conducted strictly under the auspices of part 91, in which the authority of PIC may be traded at will be common agreement between the crew).
While legally a SIC may log sole manipulator time, there is little reason to do so. By general consent, the industry doesn't recognize time spent as SIC under an operating certificate to be pilot in command time. This lends the appearance of padding one's logbook, and not understanding the legality or ettiquette of logging time.
When one is a designated SIC, one should log SIC only.
For the purposes of meeting the FAA inspectors qualifications, I would show any time spent as sole manipulator of the controls, as pilot in command time. This doesn't mean you need to change your logbooks, but you can definitely answser the question yes, in the affirmative. Should an employer ask, I would identify all time operating under a 121 or 135 certificate, when not designated the pilot in command by the certificate holder, as SIC.