alt/opt/etc boxes do not extend to encompass ref box. This should work the same way as for notes.
@startuml
activate A
alt
ref over A
Lorem ipsum dolor sit amet, consectetur adipiscing elit.
end ref
else
end alt
opt
ref over A
Lorem ipsum dolor sit amet, consectetur adipiscing elit.
end ref
end opt
opt
note over A: Lorem ipsum dolor sit amet, consectetur adipiscing elit.
end opt
deactivate A
@enduml