This seems to be new in the beta that I just installed (Version 0.99.127.2-beta (WebKit 619.1.1):
Controls should not overlap. Turning off vertical tabs or hiding the vertical tab sidepanel fixes the overlap. Unhiding the sidepanel or turning vertical tabs back on causes the overlap to reappear.
Version 0.99.127.2-beta (WebKit 619.1.1)
Sonoma (14)