1. The classic case is in Bava Metzia 115a, where there the practical difference is made clear. According to Rebbi Shimon, the prohibition of taking collateral (Mashkon) from a widow only applies to a poor widow, to whom one must return the Mashkon daily giving rise to embarrassing rumors.

2. In Sanhedrin 21a the Gemara discusses the number of wives a king can marry, and explains the opinion of Rebbi Shimon based on a logic similar to that used in our Sugya (i.e. when the Torah specifies a reason, Rebbi Shimon considers it to be more inclusive).

3. In Menachos 2b the Gemara suggests that Rebbi Shimon distinguishes between Shinuy Ba'alim and Shinuy Kodesh (for Menachos) based solely on his logic of Ta'ama d'Kra.

4. Other places where we find Rebbi Shimon suggesting a rationale for the Mitzvos are: Gitin 49b, Shabbos 23a-b, Sanhedrin 16b. (There is no clear Halachic difference in those cases.)

Note also that the Rambam in Moreh Nevuchim (3:46) justifies his position of suggesting reasons for all the Mitzvos based on the opinion of Rebbi Shimon. He goes so far as suggesting that the difference of opinion (Megilah 25a) as to why one may not say "Hash-m, you had mercy on the mother bird, have mercy on me" - depends on whether or not we accept the opinion of Rebbi Shimon.

Best regards,

Mordecai Kornfeld