There is no reason to change $/ if you are using a standard Apache configuration format. $/ is not used by Config::ApacheFormat in the literal sense of setting the variable. Config::ApacheFormat parses the files line by line and puts them into an array. It then goes through the lines by pop'ing them off the stack.
Comment on Re: Config::ApacheFormat and $/ strangeness
Config::ApacheFormat does not explicitly make use of $/. However it does try to read the conf file, line by line, via the angle operator (<>), which is affected by value of $/ (look for $INPUT_RECORD_SEPARATOR in perlvar)