It finally came a right moment to both be hit by it and have time to investigate. This blog post shares the same sentiment as I above, and confirms suspected design braindeadness.
Three selections are defined in the ICCCM:
SECONDARY, each of which behaves like a clipboard in its own right:
CLIPBOARD: traditionally used when text is copied and pasted from the edit menu, or via the
Ctrl+Vshortcuts in applications that support them.
PRIMARY: traditionally used when a mouse selection is made, and pasted with middle-click or
SECONDARY: ill-defined secondary selection. Most applications don't use it.
Be gone soon, X11, be replaced by something sane.