The encoder type is really a function of what configuration you order. If you order one with pulses per rotation equal to detents per rotation, then between detents the encoder will go through a complete cycle on both switches, so there will be a total of four transitions between detents (ignoring bounce). In the case of the PEC11s, it will end up with both switches open at the detent. It looks like the PEC9 ends up with both switches closed.
But if you look at the PEC11R datasheet How To Order, you'll see that you can also order an encoder with half as many pulses per rotation as detents per rotation. For those, a detent occurs at every half-cycle. There are only two transitions between detents, and at any detent the switches can be either both open or both closed. You can still get one encoder "tick" per detent, and determine the proper direction. So if you can get the same information processing only half as many transitions, why wouldn't you always use this type? Well, because half the time on average an idle encoder will end up with both switches closed, and drawing current through the pullup resistor. But for some types of processing, that may not matter. My writeup discusses this.
On your afterthought, I look at it the opposite way. I don't want to capture all the transitions. I want to ignore as many as I can, particularly the ones that occur during bouncing. If you use pin-based interrupts to process the encoder, servicing all the bounce interrupts may impact on your main application processes even if it detects the encoder movements correctly. My alternating interrupts system is intended to eliminate any bounce processing at all, so for a good encoder you only have to service four interrupts to get from one detent to the next, or only two interrupts in the case of the second type of encoder.
In the case of timer-based periodic polling, you can't eliminate exposure to some bounce, but you defintely do not need to poll so often that you detect every bounce. You can poll at 1 or 2 milliseconds, or even slower, and do just fine.