I suggest this:

#!/usr/bin/perl

while(<>) {
    next if /;{2,}/;
    next if /;\s{1}/;
    print unless /^\n/;
}

__END__

strip_ini.pl php.ini
[PHP]
;user_ini.filename = ".user.ini"
;user_ini.filename =
;user_ini.cache_ttl = 300
engine = On
short_open_tag = Off
asp_tags = Off
precision = 14
y2k_compliance = On
output_buffering = 4096
;output_handler =
zlib.output_compression = Off
;zlib.output_compression_level = -1
...about 300 lines more
[download]

Usage: strip_ini.pl php.ini > php.stripped.ini

Note:

;;;;;;;;;;;;;;;;;;; <-- the first next skips the ASCI art
; About php.ini   ; <-- the second next skips the explanations
;;;;;;;;;;;;;;;;;;;
[download]

The print unless /^\n/ prevents unwanted printing of emtpy lines. I don't know for the moment why they are there...

Best regards, Karl