It probably separates the two for future airline applicants. Airlines want part 1 PIC only. I.e. you are the aircraft commander / Captain.
Part 61 PIC (sole manipulator) is good for building PIC for higher ratings (ATP), insurance requirements, etc. Corporate operators will typically accept part 61 PIC too as they are concerned about insurance requirements. You can log part 61 PIC anytime you are manipulating the controls and are appropriately rated in the aircraft. Appropriately rated means having the type rating (or NATOPS check for military) if it is required.
I have long advocated military pilots that have any thoughts of flying civilian keep their own logbook in addition to their military one. Civilians log block out to block in vice takeoff to landing (i.e. more time). I have also advocated keeping two PIC columns, one for part 1 and one for part 61 for the ease of filling out future employment applications or FAA license applications. And yes, you could double log some part 1 PIC under part 2 also. For example, a P-3 PPC would log the entire flight as part 1 PIC and his pilot flying / first pilot time as part 61 PIC. (I personally only used the part 61 column when the part 1 coulm was blank. This way I could add the part 61 time to the part 1 time for insurance, corporate and FAA while keeping it straight part 1 for the airlines.)
And also yes, that same PPC can log the time he is in the rack as part 1 PIC because he is still the aircraft commander. so for a 12 hour flight, in his civilian log it would be 12 hours total, 12 hours part 1 PIC and 4 hours part 61 PIC (I personally would not log the part 61 time in this case)assuming 3 pilots on board. The 2P (NATOPS qual) would have 12 hours total, 4 hours part 61 and 4 hours SIC. The 3P (non-NATOPS qual) would have 12 hours total and 8 hours SIC.
There is even a valid argument in the civilian world that the 2P could log 8 hours SIC and the 3P 12 hours since they are required (by the Navy) crew members and the FAA says you can log the time if a required crew member regardless if you are in the seat or not. In fact, at my airline when we fly with more than 2 pilots, the airline gives the pilot credit for all the time when they calculate our flight time. The Captain gets PIC and the other pilots SIC.
Do a search on the site. We've discussed this issue many times before.