katsklaw has more then enough knowledge about the technical background to make his points... and each one of them - with the exception maybe of nr3 - is valid.
Nor cs_join, nor ircd_init respect the BSMinUsers settings.
The result is that while bans and modes may be cleared by anope internally, they will not be cleared by the ircd because it still sees a client (ChanServ -which is invisible to services).
Simply example... some1 bans an op, all real users leave channel and only chanserv will be left. at this point services will thing the channel no longer exists and the op will be unable to unban or invite himself in through chanserv because it things the channel doesn't exist.
This doesn't mean that it s impossible to create a module that puts chanserv in channel, but all modules currently around will cause this kind of desync since they fail to properly handle this kind of situations.
Just because YOU have not seen any problems doesn't mean there aren't any...