How can I use pre declared blocks in a php file?

You can use do_blocks and insert block content as string in that function, which will like do_shortcode transform block’s html and metadata in html comments into final html.

I am not sure if it works for reusable blocks, I never used them.

If you want to use block theme, you should develop your own blocks for any missing features. This is nowadays much easier than it used to be, you can tweak existing blocks, create block variants, block styles, enqueue extra style for core blocks (wp_enqueue_block_style) etc.