I have two preferred layouts saved in the layout manager.
Horizontal: Split horizontally. Outliner on top, editor on bottom. Binder selection affects top (nongroup in other).
Vertical: Split vertically. Editor on left, outliner on right. Binder selection affects right (nongroup in other).
However, switch layouts, panes always opposite of what I want. The editor ends up on top, or on right, and outline on wrong side I have to use Swap Editors, or click the binder to re-open in the right pane.
I know why it does this (I can’t put into words), but way to not do this?
I think the fundamental problem you are running into is that there is an underlying assumption about the top and left splits being connected, or considered the same thing, in different orientations. Thus the bottom and right are similarly connected. We have to choose to connect one or the other, in other words (else it would be chaos, a flip of the dice whenever you swap orientations), and this is what made the most sense since those two layouts are the most common and conventional approaches in software that has a less fluid design.
As for that convention, most three-pane software, or even web apps, works this way: what one clicks on in the left sidebar loads in the top or left (like the contents of the inbox you clicked on, as a list of emails), and then what one selects in that view (like an email) loads in the bottom split, or further to the right.
So again, we had to choose something to have a consistency when swapping, and following what is most typical made sense. Setting things up so that you are following the convention in one layout (left→top→bottom), but the opposite for the other layout (left→rightmost→middle), will cause the content within the splits to “flip”. The only way to avoid it is to follow the conventional layout for both orientations.