Layer Order is Reversed when Auto Layout Removed?

Hi! Hoping I’m missing something obvious and that this isn’t an intentional thing.

Sometimes I use auto-layout temporarily to tidy things up, and sometimes I just change my mind and want to remove the Auto Layout after adding it. But for some reason, whenever I remove it, the order of the layers is reversed no matter which Canvas Stacking option I have selected.

Is there a way to change this setting? Or am I missing something?