You tha masta!
Well, all together, to fix this mess I did:
Manually, in the xml project file, made sure that my problematic sprite has UID 1 (by swapping its UID with the one that had the UID 1)
Created a new subfolder in my "layouts" folder, named it AAA (you can't place layouts before subfolders)
Place my placeholder layout into that AAA subfolders. That placed it on top of the list
Well, let's not sing victory quite yet, I was already sure to have fixed this a couple of times, but it always fell down at some point