Hatmana would lchoira be similar to playing something wrapped in foil into the cholent according to most of the svaros mentioned in that tumult. RSZA is matir among many others.
It is totally dissimilar. Over there the intent is to have the transfer of taste between the kugel/kishka, it is therefore similar to a potato in the Cholent or a Kneidel in the soup. If that is not the intention, and there would be a complete separation, the Aruch hashulchan indeed writes that it would be prohibited.
. Even among the machmirim this may be included in the svara of Minchas Yitzchok that when it is the way to cook it we would not call it hatmana.
I assume that what אנשי טבריה held when they put the סילון in חמי טבריה. But the Rabbis didn’t agree. So how is it different?