rationalfrummie,
I am admittedly a beginner at learning gemara. From the way I have understood of bedikas chometz and bittul chometz, I personally do not see a contradiction in the Rashis you provided.
1. Nullification is sufficent to fulfill the d’oraisa requirement regarding chometz (Tosafos above)
2. If nullification is done alone, however, there is a risk that the person will later come across some chometz that he finds very difficult to consider nullified, so a bedika should be done as well as nullification derabbanan. (1st Rashi)
3. No contradiction in the 2nd Rashi if he sees the bedika as d’rabbanan.
4. On the other hand, bedika should not be done alone, because it would be very difficult to be sure you got everything (2nd Rashi).
Does this make sense, or am I not understanding something correctly?
Have a good Shabbos!