The Gemara concludes that we are meant to conduct ourselves stringently regarding the two opinions of bein hashmashos (i.e. melacha on Motzei Shabbos can only commence after the conclusion of the later bein hashmashos). Since bein hashmashos in itself is a period of uncertainty (safek day safek night) why is melacha not permitted during the later bein hasmashos since it is a double safek (safek sfeika) 1) maybe this moment is already past the real bein hashmashos 2) maybe bein hashmashos in itself is really night; as we know a double safek in Torah is permitted?
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A speculative Terutz: We are left with two opinions. One is Machmir during the first Bein Hashmashos and one during the second. We are Machmir to keep both. There is nothing else to that Shita other than to be Machmir. You can’t take the Shita and throw out what he holds.
More to the point: The Tosafos in Nida 27 (first Tosafos) explains that we can’t use a Sfek Sfeika both ways, to be meikal on both ends. As in our case, you would use the Sfek Sfeika to our benefit to push off Shabbos until Reb Yosi’s Bein Hashmashos, and then end Shabbos early or eat Teruma early by moving up Bein Hashmashos to Rebbe Yehuda’s. Therefore we are Machmir instead.
Besides, it is really only one Safek, if it is night. There might be many ways you can reach a conclusion of the facts, but they can’t necessarily add up to a Sfek Sfeika. We can say, the whole Bein Hashmashos might be of one day, and even if it isn’t, now might still be from the day. Obviously, we don’t do that, since essentially the Safek that we are having is one Safek, is it currently day or night.
Perhaps Bein hashmoshos isn;t a classic safek, but has a “din safek” . As such we cant utilize sfeik sfeika, as it isn’t a “doubt” but a briah that hashem made in the world with a din safek.
Also perhpas not knowing how to pasken isn;t a safek. it isnt like a safek if meat is treif or kosher, this is a safek of how to pasken in general.