You bring up some good points, but due to privacy issues, even though you can find out how many shares are shorted, it is very difficult to find out who the owner of these shorts are. You are correct, whoever is accumulating shares even in an agreed takeover situation must file a 13 D form within 10 days of accumulating over 5% of a public company even in an agreed takeover.
Now the strange thing, is that they can also file an abbreviated version of this(13 G) which allows certain institutional investors such as registered investment companies/banks etc., which allows them to only report their holdings 45 days after year end....and in this case I assume that Ampersand and company would qualify here as so far they have not reported their holdings via a 13 D, and I am certain(OK almost certain) they already control enough shares to swing the vote in favour of the takeover.
So that brings us once again to why the registered shorts have not covered, and who would benefit from this? And this would depend on who owns and controls these shares......again, not sure if this matters at this point as I believe this is a done deal unfortunately!