In phase and out of phase are both terms that can mean a number of different things. You're thinking that the physics of a ported enclosure are similar to a transmission line when it really isn't. In order for the rear wave to be in phase with the front wave, it's going to need to travel quite a long distance, even at higher frequencies. That's what's happening in transmission line enclosures. The line length is set to either 1/4, 1/2, or 3/4 the wave length of the Fs of the driver you're using. Ported enclosures do not use 1/4 wave theory but rather, they're based on Helmholtz resonators. At tuning, the enclosure is set into resonance which drives the air in the port to move in and out. This mass of air stimulates the air outside of the enclosure and causes a change in pressure just like the cone of a sub does when it moves in and out.
This mass of air is what causes the majority of output at the tuning frequency. The sub also plays a role as the driving force and also adds to the output. These two moving objects are not going to be 100% in phase with each other. They will also not be 180* out of phase either. There will be a slight delay between the two but the delay will usually be in milliseconds and should be small enough to not cause any audible losses.
If you're still lost thinking that the slight difference in phase would cause all sorts of issues, think about it like placing two speakers directly in front of you but put one about a foot further away than the other. Then listen to music and see how it sounds. Then place the two side by side and play music. See if you could notice a difference. The two drivers would be slightly out of phase from each other by the time the sound reached your ears. It's the same idea here. Now if you placed the two speakers 1/2 of a wavelength and then played that frequency, you would hear a noticeable difference in the sound.