How do I filter the excerpt metabox description in admin?

This description is generated by post_excerpt_meta_box() function and is not passed through any explicit filters. It is however echoed by translation-related _e() function and so passes through gettext filter (which from your question you are already familiar with).

As for limiting it to your CPT, I think current post type in admin is held in global $post_type variable you can check.

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