Embedding Linked Illustrator content should embed the native content instead of the PDF version.
When you place a Linked Illustrator object (from a file or from a CC Library) and later decide to Embed it, you actually embed the PDF content of the linked file. This results in many groups, clipping masks, reduced editability (no Appearance effects, Symbols, Brushes) and loss of layers.
The optimal editable way would be to embed the native objects instead of the PDF version, similar to Copy and Paste with the Paste Remembers Layers option turned on.
Ton
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Mark Gould commented
Please consider voting for or merging with this idea:
Either way, I don’t understand the benefit to the user of placing a linked object when it results in the behavior of multiple unintended clipping masks, etc.
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For some time now, saving an object or group to CC libraries and then placed back into a document ends up with not one, but two layers of clipping masks. If I save an ungrouped single path to a library it comes back in grouped with these clipping masks – the workaround is to "place copy" of the graphic which avoids this behavior. But I can't imagine what the desired result of placing the original with clipping masks would be. I've had this issue through multiple versions, and the same behavior repeats on the current Ipad beta, since you don't appear to have the choice to place a copy of the library graphic, just the 'clipped' original. Not sure why placing the original graphic from CC Libraries results in these double clipping masks.