Joseph, Rav Moshe does not say that. On the contrary, he says that in our time someone who desecrates Shabbat does not do so because he has renounced Judaism but for some imagined benefit.
Rambam (Hilchot Mamrim 3:1) says that the Karaites in his time were condiderd tinokkot shenishbu because they were raised in their beliefs. This is exactly analogous to today’s non-observant Jews. They truly believe that religious commandments are optional. Non-observant coworkers even used the words “prohibited to you” . The Rema (YD 340:5 in the name of the Or Zarua) apparently rules like him.