A49 & 50
Yes and yes. The same effect with differing results is refering to an effect that is incompatible with itself (hence why it says usually, as many effects are incompatible when cast twice for differing results, but not all), for example, if you cast polymorph twice. You can only have a single form, thus the second overwrites the first in this case. As it also says, the first spell is still in effect, and so in the case of resist/protection from energy, both spells are cast, and you are most certainly capable of having resistance/immunity to more than one kind of energy, so they both remain in effect.
The "One effect makes another Irrelevant" clause also does not apply, as neither make the other irrelevant in either case. This only comes into effect when you cast Resist Energy (Cold) and Protection From Energy (Cold) which is also explicitly called out in the spells themselves, indicating how they interact.