I know, why would you. A PDF-layer is basically a composite flattened layer Ai writes into an .ai document, and just reads it when the file is placed: in Photoshop, in InDesign. Handy, yeah?

Not really. Saving a document without the compatibility is so much faster. The non-compatible files are so much lighter (especially with heavy raster links used within). OK, Ps and InD can’t read PGF (Progressive Graphics Format, the one that’s native for Ai)... but Ai can.

Why not reading linked .ai docs as they are and THEN keep it’s PDF representation within the destination file, if it makes the difference in performance? I don’t mean save this representation within it, just regenerate it on opening, no?

I mean, I’m so tired of seeing these 'This is an Ai® file that was saved without PDF...' stamps instead of actual content when I need to link something... instead of generating it right there and now, you force us to import/open the link, resave it and try anew. You can read these! Just read them, please.