Personally I'd do the first operation (or two) somewhere else, not the last. The press's weakest spot is probably the priming system. Consider that and check this out.
I don't know if it is possible on the Pro1000, but the best luck I had with the Loadmaster was decapping and priming off-press and then doing the rest on the press. Well, I say "off-press"...what I actually did was I had two toolheads for each caliber - one head had just the caliber-specific decapping die in it, the other head had the rest of the dies. I'd take a couple hundred cases and run them through the LM and decap them all. Then I'd prime all the cases with the Lee hand priming tool. Then I'd run all the cases through the LM again (using the other toolhead) and flare, powder-charge, bullet-seat, and factory-crimp. This worked pretty well but I got to handle each case 3 times, which sucked.
A better way would have been to get a Classic Cast single stage and run all the cases through that first, using a universal decapper. I'd also go ahead and prime on the Classic Cast. Then I'd run all the cases through the LM to flare, powder-charge, bullet-seat, and factory-crimp. This would mean only handling each case twice.
Anyway, like I said, I don't know if the Pro1000 would support this kind of strategy. But if it did, then the 3-station setup would still let you factory-crimp. Just a thought.
-cls