On a typical HHD, under typical circumstances, all writes go to the SSD, and are copied to the HDD later on. So far so good; Apple's solution will do the same thing. And stuff being read gets copied to the SSD in both cases. Also great.
That's an assumption we've yet to see confirmed, and I suspect is incorrect. I doubt every single file that's read will migrate to the SDD. Rather, I expect only files frequently read will migrate to the SDD. Effectively, the SDD will largely be a write cache (but likely only for files written atomically) and a read cache for frequently accessed files.
That behavior would largely sidestep your concerns.
(And, actually, files that are readily streamed, like videos, aren't necessarily files you'd want to store on the SDD. Those can often – though, yes, not always – be read quite quickly from the HDD. Unless you're dealing with truly huge files, or actively editing a video, you don't need SDD throughput.)