The root cause may just be the increase in dead space caused by mobile first UIs.
The author looks like they've only looked at the color of the dead space so probably not significant for this specifically.
The trend against skueuomorphism maybe equally relevant: that early example is a descendant of Apple's previous brushed-metal UI. Though even among the flat ones there's been a trend toward lightening.
It'd also be interesting to see what area the author picked on each screenshot: a big difference, at least before Tahoe, if you decide that the Finder sidebar or top bar is what you're going to look at.
No.
The reason Light Mode has been getting lighter is simple: because the default computer in 2025 is now a laptop or phone, whereas in 2009 it was a desktop.
Laptops and phones have easy and relatively coarse brightness adjustment settings for their screens. Desktops didn't, and still don't.
So it makes sense that you'd just make whites as bright as possible- if the user doesn't like that, they can just turn the brightness down. Otherwise you're just kind of leaving the monitor's available/potential contrast on the table.
Note that Dark Modes skyrocketed in popularity after the default computer changed from being a desktop to a laptop- but that's because laptop and phone screens couldn't (and still can't) get dim enough at night (for dark colors are still bright due to inherent backlight bleed-through).
The next change to this trend will occur, specifically to Dark Mode, 1-2 years after the average machine a software designer is issued for work has an OLED screen- because OLED screens actually can get that dim, the current color balance will likely be inappropriate.