Did they ever fix PCIe over thunderbolt security?
It seems to depend on whether you're on a desktop or mobile device. [1]
macOS 13 Ventura was released in 2022 and for portable Macs with Apple CPUs Apple introduced a feature known as ‘Accessory Security’ (also known as ‘Restricted Mode’)
By default, portable Macs (i.e. laptops) with an Apple CPU running macOS 13 Ventura or newer version of macOS will require the end user to authenticate and approve a Thunderbolt device when initially connected.
Stationary Macs (i.e. desktops) with an Apple CPU running macOS 13 Ventura or newer version of macOS do NOT implement the ‘Accessory Security’ feature. As a result, Thunderbolt devices will be automatically approved and authenticated when initially connected.
Anecdotally, I have had Dell and Lenovo laptops with Thunderbolt and in Linux I had to manually approve each new device before it would function. [2]
[1] https://kb.plugable.com/docking-stations-and-video/do-i-need...
[2] https://wiki.archlinux.org/title/Thunderbolt#User_device_aut...