In summary, "&$reference" means "do-not-copy-on-write the value here, in perpetuity". Assigning by reference is not assignment, it's "make &$variable a reference and its value do-not-copy-on-write, in perpetuity, and make the variable I'm assigning to use that do-not-copy-on-write value as well".
To "unreference/unalias" you have to either unset or make an explicit copy into a new variable.
Object properties that are references will survive cloning and remain references. Generally the same is true with references in arrays and PHP's array functions (combine, intersect, call_user_func, func_get_args, etc).
Calling a function that uses a reference parameter will *make* the supplied variable a reference. This is also true when using variadic array expansion for arguments; the supplier's array element will become a reference.
Generally, don't use them unless you're dealing with low-level calls, or need an accumulator, etc. For poorly designed functions that use them, give them a copy to mangle.