The layout has improved, here is the list of new features and a bug fixed:

• merged buffers are now supported in layout: WeeChat will auto merge buffers when they are opened and on /layout apply
• the layout for windows and buffers is automatically restored after /upgrade (not the layout saved, but the layout you had immediately before doing /upgrade)
• an old bug was causing bad order of buffers when connecting to many servers at same time, and then /layout apply was required after starting WeeChat

Enjoy!