I've never used PDF::API3::Compat::API2 myself, but as it says Compat::API2, I guess the idea is to be able to do it like you would in PDF::API2 — which would be:

use PDF::API2;

my $pdf = PDF::API2->open('uncropped.pdf');
$pdf->cropbox(100,100,500,500);

$pdf->openpage(1);

$pdf->saveas('cropped.pdf');
[download]

The crucial thing is to open the respective page(s), as the cropbox will only have an effect on newly rendered objects, i.e. objects opened for modification.

Here are the PDFs — for reference, or to play with: uncropped.pdf, cropped.pdf