I grew up on the Birnbaum siddur, I admit it. I read the little explanations at the bottom of the page over and over. Later, I bought a set of Artscroll machzorim and used those on Rosh Hashana and Yom Kippur. I never tried to compare notes, but this morning, something struck me.
In musaf on Shabbos, we say a kedusha which is different from that of Shacharis. The Birnbaum says that the insertion of the shema is the result of a 5th century practice by government forces intent on eliminating the statement of hashem's unity of putting "spies" in the shul to ensure than no one said Shema. At the end of davening, when the spies were gone, the Shema was said by being placed in the kedusha. This means that it was a decision made by religious authority to innovate a new text. (that's a recap and extrapolation from the write up on page 394 of the Siddur Hashalem.) While I haven't researched this, I'm assuming that the Birnbaum people didn't make this up from no where.
We say this same form of the kedushah on Yom Kippur in shacharis. The Artscroll machzor explains (page 406-7) that the kedushah in this form reflects a higher level of holiness which we attain usually only at musaf but which we are at in shacharis on Y"K. It also says that the text comes from Pirkei DeRabbi Eliezer (chapter 4, at the end, page 8, here http://www.daat.ac.il/daat/vl/pirkeyeliezer/pirkeyeliezer02.pdf). Though it doesn't give a start date for this practice, the text was written (according to wikipedia) any time from the first to 8th century CE. The inclusion of Shema was then NOT related to spies, but to a totally separate claim to holiness.
The easiest reconciliation of these 2 versions is simply to say that one is wrong so if anyone has a good piece of scholarship which clarifies, then pass it along. Otherwise, I am wondering why there are two diametrically opposed explanations for a text's source.