Squirrels (below) seems to think otherwise, so we have contrasting answers.
Decided to have an experiment, I downloaded one of my own schematics from the alternative download location and refreshed the page, it did not increment from 14 to 15. Though maybe me being logged in and it being my own schematic affects it. Or it just only updates the count every now and again.
That said, there are submissions on the front page, with ONLY the alternative download that count some amount of downloads, which is odd if it isn't counting them. And I checked multiple sources so it's unlikely to be one that had a schematic link there but since removed it.
The evidence for it does count externals downloads seems a bit more compelling to me, but i'm still unsure
UPDATE:
Nevermind, it has just incremented to 15. And I'm pretty sure it wasn't someone else since the download on it haven't changed in about 2 weeks. Seems it just takes 2 or 3 minutes to change. So I think it is correct, that it does count the alternative download link
