General questions on Surnames/Family Names

My fist question relates to the 'evolution' of surnames (in Bavaria) as recorded in RC church books (commencing approximately 1650). The surname spelling changes frequently (recorded by scribe/priest based on how they "heard" the surname) ..a child born with surname of Mössner, is married with surname of Mössmer and dies with surname of Mösner (and several other variations Messner, Mesner, Messmer, Meßner, Meßmer , Mößner, Mößmer). Children of a couple frequently have differing surnames from their parents and each other - more than likely due to the phonetic spelling. I have been recording the surname at birth (birth surname) but in sources record the surname as recorded by the scribe / priest. At one point, I was using the Also Known As but with the many variations of the spelling it becomes unwieldly. This results in 'conflicts' (I just hide these as the information is accurate and well sourced). The worst part is attempting to use the 'Go To' function to quickly locate a profile .... Is there a 'best practice' for surname evolution?

Deanna