You are welcome to make the php.ini look however you'd like on your machine.  Realize what you're asking is not really a PHP issue, but an administration issue.  We distribute PHP with a list of recommeneded php.ini values, if you change them, how you keep track of them is your choice.  You can, for example, do something like this....

Original will look like this:
foo = 45

Your changes can be kept track like so:
foo = 33 ; 45 | seconds

anything after the ; will be kept as a comment.  

I realize your point, however, I feel that quality documentation out-of-the-box is not an unreasonable request. Many users trying to configure php for the first time (or even subsequently) have problems deciphering some of the options, and even the comments, which can be vague. For instance, 

; The path for which the cookie is valid.
session.cookie_path = /

It is unclear if this means the path on the local machine, the path as seen by the browser-agent, etc.

In addition, consistency in the file would also be preferred, for instance, why is
session.gc_maxlifetime in seconds
session.cache_expire in minutes
max_execution_time in seconds

output_buffering in bytes
memory_limit in megabytes
post_max_size in megabytes
odbc.defaultlrl in bytes
(other db configurations) in bytes

its a minor thing, but still consistency is important.