There are some kinds of changes where you won't know if they work until you try it on a test system... or in this case a live system... this isn't one of them. CGI is (still) in the Perl core, so this one is particularly easy to test locally.
use CGI ':standard';
my @cssFiles = ("src1");
push @cssFiles, "src2";
<link rel="stylesheet" type="text/css" href="src1" />
<link rel="stylesheet" type="text/css" href="src2" />
<!--/* <![CDATA[ */
/* ]]> */-->
So that's a yes, frozenwithjoy's suggestion should work, provided you use an array reference (-src=>\@cssFiles, not -src=>@cssFiles).
If you had a test system, even if it's not an exact mirror of the live system but at least can execute your code, may have saved you the ~20 hours wait on a solution...