Is there a reason why an autotransformer (Variac) should not come after a true isolation transformer?
Yes, the autotransformer has moving parts and exposed conductors so there is greater risk of accidentally rereferencing the output voltage to ground either by short or by leakage. Although the energy will be limited, this still poses a potential shock hazard or DUT damage if you were relying on the output being isolated from ground.
There are some bench products that are exactly that, such as B+K Precision 1655 and Sencore PR57 and PR570.
The BK1655 and PR57, at least, are wired with the isolation transformer last, going more or less directly to the output sockets. I haven't seen a PR570, but I'd presume they haven't changed the layout.