I'll hook into this thread, as I don't want to open another one.
I too quite like the option to set a reference object to which the selection is then aligned – deselecting and selecting again seems a bit counterintuitive to me, though a useful workaround.
But my other (and worse) issue with the align tools is as follows:
In Publisher 220.127.116.11 on macOS 10.14.2, I added all the align buttons to my top toolbar:
When I use those, they seem to always default to "align to spread" with one selected object and "selection bounds" with multiple objects selected.
Is there a way to control what alignment mode the buttons work in? I'd like to reduce having to go into the overlay-menu of the single alignment button.