The 1.32 beta has solved my issue with hiding notification area icons when taskbar is 2 rows.
However, I still get a scrambled desktop whenever I activate taskbar autohide.
I had a thought of rearranging the desktop icons to normal/desired while in the autohide mode, but that presents a new issue that is still present in the beta. When autohide is switched on, the taskbar goes to one row and is locked that way. I have to turn off autohide, then turn off Lock all Taskbars. Autohide and multiple taskbar rows are mutually exclusive.
So, even if the icons were staying where they need to be, I’m back to my original issue of not being able the set the taskbar to 2 rows.
FYI, my target is an autohiding taskbar that is 2 rows high and all the desktop doesn't get scrambled.
I posted screenshots in thread at https://forums.stardock.com/512300/system-icons-disappear-from-notification-area-when-taskbar-is-more-than-1-row