Getting deeper into theory hearI admit half baiting you into this question because I wasn't expecting an answer that would be legit.
This isn't true in the way you think it would be. Ports are slightly out of phase with the driver that is feeding them to begin with. Can you hear it? Actually no, you hear numerous things but not the phase part. First you must understand that a driver is out of phase with itself constantly. Every frequency moves the driver a different amount because the size of the frequency is different. Because of this the frequencies cannot have the exact same phase, since the sound is originating from different points. To listen to a speaker of any kind is to hear varying phase.
What you're hearing is modes, caused by overlapping phase, but you aren't actually hearing the phase itself - you may be hearing the character of the ported subwoofer as well. This will happen with any subwoofer. Obviously using a crossover to reduce the overlap helps but this isn't specific to ported or any other form, it's source/amplifier dependent. When you adjust a subwoofer's phase (amp/preamp/crossover) you aren't perfectly aligning it to the mains to have same phase (no such thing), not in any way what-so-ever, you're simply getting to a mode/node point that is least offensive so that it sounds right.
And ported speakers don't always have a bump, but you do see it often. There is no specific reason why they would have to have a bump - I've seen lots that roll of very gradual.
Well, it's not true so...
First, WRT ports being "slightly OOP" primarily depends on the placement of the port, not only the mechanics and the resulting OOP sound as it escapes the port. So there is no definitive amount to quantify "slightly".
Second, just because a bass driver (in our case) is reproducing hundreds of frequencies which are OOP they are all time aligned relative to the driver. And while there may be modes as you call out, it's the speaker designer's job to assess and engineer the driver, xover and cabinet to avoid such audible challenges. Coaxials have a problem mitigating such issues.
Third, WRT, "What you're hearing is modes, caused by overlapping phase, but you aren't actually hearing the phase itself", how else would you hear phase anomalies other than cancellations or augmentations at overlapping frequencies?
Finally, WRT, "When you adjust a subwoofer's phase (amp/preamp/crossover) you aren't perfectly aligning it to the mains to have same phase (no such thing), not in any way what-so-ever, you're simply getting to a mode/node point that is least offensive so that it sounds right."
Yes and no. When you adjust a subwoofer's phase you can almost perfectly align to the same phase as the mains if the sub(s) proximity is aligned to the mains (like done with tower designs with separate bass / sub columns). However, this often times exacerbates room modes by injecting even more bass from essentially the same location.
Your second point about , "You're simply getting to a mode/node point that is least offensive so that it sounds right." I wouldn't say this is quite accurate. Your mains' bass rolls off (sealed or ported), ideally you want to roll in your sub to avoid that audible roll off and continue to provide subterranean bass (we all know this). By adjusting the subwoofer phase you are looking to align the phase response of the sub to the mains at the critical mains' rolloff frequency to fill that low freq trough while being mindful of room modes exacerbated by mains and sub placement. With everything in audio, it's all a compromise.
Also, almost no room permits, "perfect phase alignment". Sounds are constantly interacting exacerbating and attenuating frequencies, that argument isn't only indicative of bass frequencies. It's also simply part of nature.
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