is there some way to Merge down basic layers?

[Ofnuts]

You can use Edit > Paste as floating data (and perhaps reset the Ctrl-V shortcut to it) to get the old behavior.

In modern Gimp, the floating selection is generally considered a nuisance, it was a cop-out when RAM was scarce. Now you mostly keep your layers distinct, merging is easy, separating is often near impossible.