Yes, the solution is as simple as removing the trailing ".exe" extension
in the preferences. However, it's something that should work out of the
box, given that autopano-sift is in the repositories.

And, now that we are there, shouldn't hugin suggest or recomend
autopano-sift? There's no need for a dependence, since its use is an
optional step, but a suggestion would be nice

** Changed in: hugin (Ubuntu)
       Status: Unconfirmed => Confirmed

-- 
Hugin references windows binary autopano.exe
https://bugs.launchpad.net/bugs/81255
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