I'm pretty sure the only context where that cookie is used at all is when using foldersites and when not using related sites mode, so I would not expect that we need to put that code elsewhere.
authentication cookies are scoped to the host name, so there is no cookie collision if using mutli sites based on host name.
when using folder sites the same authentication cookie is shared across sites because the asp.net framework does not make it possible to dynamically choose the cookie name at login time. when using related sites mode then all folder sites share the same users and roles so we also don't need an extra cookie there, if a user logs into one site he is logged into the others.
but when using folder sites and not using related sites mode we use this extra cookie to determine if the user is really logged in to the current folder site and we have a custom Principal where we check for this cookie in that case.
I don't think that cookie gets set at all in other scenarios so it is hard for me to imagine we need to clear that cookie in any other scenario than in folder sites not using related sites mode.
Actually the code above it is supposed to "expire" the same cookie but was probably written before we had that cookie helper method.
I'm not opposed to moving it but it seems like it is in the correct place.