This is an irrelevant example, Ibn Mas`ud's time was different than ours, in his time there was no ONE standard Mushaf, each person had his own Mushaf, during `Uthman's time there was a project to unite people upon one Mushaf to avoid conflict and problems. Although this project resulted in a better compilation, still many folks held on to their own Masahif and recitations, with the passing of time those different Masahif and recitations would be dismissed and everyone would adopt `Uthman's codex.
Let's make the comparison clearer:
Ibn Mas`ud simply had an opinion that those two last small chapters were supplications, not necessarily a part of the Qur'an. He didn't believe the Companions changed it intentionally, nor was true revelation lost, the book was intact in his view, the people around him were free to believe what they wanted since the vastv majority of people never had a full Qur'an in book form lying around in their houses. The reason Ibn Mas`ud believed this, is because he must have heard the Prophet (saw) say so, it's very possible they were merely supplications initially then God made them a part of the Qur'an due to their importance in people's lives. Or they were Qur'an from the beginning, the Prophet (saw) recited them as supplications so Ibn Mas`ud didn't know they were actual Qur'an. Eitherway, he changed his mind later in his life when he was faced with multiple evidences, that's why the recitation that reaches us through his chain contains the two chapters.
The Shia scholars on the other hand came many years later, AFTER the Qur'anic text became popular in its current form and agreed upon by the nation. They said certain verses/chapters were intentionally removed by the Companions, guidance was lost, the text was eternally corrupted, there's no way of accessing the true revelation/knowledge. Those Shia died insisting on this belief and propagated it to their followers today.
That's a HUGE difference.