Asciidoctor PDF does not support arbitrary passthrough content. While the basebackend for the PDF converter is html, it only recognizes a limited subset of inline HTML elements that can be mapped to PDF (e.g., a, strong, em, code, etc.). Therefore, if your content contains passthrough blocks or inlines, you most likely have to use a conditional preprocessor to skip them (and make other arrangements).
Here’s an example of how to skip a passthrough block when converting to PDF:
ifndef::backend-pdf <script> //... </script> endif::
Here’s an example of how to only enable a passthrough block when converting to HTML5:
ifdef::backend-html5 <script> //... </script> endif::