But there are a number of times where explicit copy/paste is much nicer.
I don't know what DE you're using, but in KDE, both modes work, and they go into different buffers. So if you feel the need to do the explicit copy/paste with Ctrl-C/V, it works fine, and you can even highlight something else afterwards, then paste the two separately with middle-click and Ctrl-V.
No, having one buffer is not better in any way. It's stupid in fact. Better is KDE's Klipper, which keeps a history for this buffer and lets me choose things I previously highlighted or copied.