I assume that your question is that we poskin that Shma is D’Orayos and that therefore sofek D’Orayso Lechumra.
That being said, R’ Moshe writes that the Chofetz Chaim poskined like the Gra [and that the Gra poskined like the Gra].
The Chazon Ish also poskined that we can rely L’chatchilo like the Gra.
So perhaps the real question is why the Chazon Ish, the Chofetz Chaim and R’ Moshe did not think that this was a sofek and poskined L’Chatchilo like the Gra.
R’Aharon Kotler and the Steipler were makpid on the zman of the Mogen Avrohom. Do you think it is a problem for people who rely on the psak of the Chofetz Chaim, R’ Moshe, and the Chazon Ish?