Results in a Response Spectrum analysis are the peak response over the entire event. Though this analysis uses Modal results, the output is not by frequency, it is the peak response due to all frequencies in the input spectrum. This is different than a Harmonic Response analysis which has output by frequency. Hopefully this answers question 2. Why must the response be greater than the input spectrum? For example, say you have an input spectrum that peaks at 3 Hz and drops to zero after 30 Hz, but you have a structure whose first mode is at 300 Hz. In that example, the output response is going to be practically zero.