The Gemara goes through a lengthy discussion about when Shabbos is kovai'ah something for ma'aser -- i.e., is Shabbos only kovai'ah something whose processing is finished or also something whose processing is not finished. My questions is, isn't something whose processing is finished already kovai'ah for ma'aser? Isn't finished processing (nigmar melachtan) the time at which foods are kovai'ah for ma'asser? Assuming that is correct, then how can the Gemara ask whether Shabbos is kovai'ah only for foods which are nigmar melachtan or also those which are not nigmar melachtan, when Shabbos is NOT what is kovai'ah the foods which are nigmar melachtan? The fact that they are nigmar melachtan is what is kovai'ah those foods!
"Nigmar Melachtan" (processing is finished) alone is not Kovei'a a fruit for Ma'aser. The Chiyuv of Ma'aser needs Nigmar Melachtan plus Re'iyas Pnei ha'Bayis (it must be brought past the threshold of one's home) in order to be Chayav in Ma'aser. See RASHI, end of DH Tinokos, who clarifies your point.
You are correct that there are times when Re'iyas Pnei ha'Bayis is not needed. But Nigmar Melachtan is never Kovei'a by itself, but only when there is another condition (of which there are six altgother) together with it, as described in the background section to this Daf.