Precedence discussions aside (it didn't seem like you need precedence levels here), your problem is that you're only trying to match two things in a binary_op. Binary ops are more like "chains of one or more expressions of equal precedence", and since you only seem to have one level of precedence here, we can just do a loop:
binary_op : '(' subexpression (op subexpression {[\@item[1..2]]} )
+(s?) ')'
{ [ \$item[2], map { \@\$_ } \@{\$item[3]} ] }
If you want to be able to have an alternative that doesn't need parens, just mirror the same rule without parens. Let me know if you still have trouble...
P.S.: When writing PRD grammars, its useful to use a non-interpolating heredoc (e.g. my $grammar = << '__ENDG__') so you don't have to backslash anything. :)
binary_op : '(' subexpression (op subexpression {[@item[1..2]]})(s
+?) ')'
{ [ $item[2], map { @$_ } @{$item[3]} ] }
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