Guides are a bit of a crutch, and smart guides are often a hazard (precisely because of mathematical versus visual centering being different in many cases). They're useful to check later if things line up to the pixel, but they don't help with e.g. creating rhythms between leading and images to find the perfect line height to match the perfect image width/height so that the top and bottom of an image aligns with the ascenders and baseline of the text that flows around it. Guides will not decide for you which element something else should line up with, nor which side of an element to align. Sometimes aligning the left edge of something with the center of something else is appropriate, for example.
It's true that small imprecisions in lining things up create subconscious disruption - but most people who've done years of design can spot a 1px misalignment like that without guides. The rule that everything should line up with something else doesn't refer to technical precision. It refers to how you construct and think of where to place each element in your overall design, well before you get to the stage of pixel-level adjustments.
Guides are not a 'crutch' they are the invisible framework of the page.
Guides might be a problem or inhibiting in classical design, but not web design where breaking the rules set by the guides will usually cause problems.
That's because designers use guides. Things that line up with guides, line up with other things.
So putting it as the later, aka 'lining up with other things' becomes rather the indirect way of putting it.