I'm not a Cubase user so these answers are more general but...
1. It shouldn't
make any difference unless you have a plug-in that uses some kind of separate timing input
that will only work in real time. I can't think of any off the top of my head but I seem
to remember hearing that certain obscure plug-ins only work properly in real time.
2. You're possibly seeing inter-sample peaks. Certain waveforms can be sampled
before and after the true peak value with the samples giving legal values but the actual
value of the peak can be much higher than the samples. In normal playback the true peak
value will only be realised when the signal has passed through the DAC's reconstruction
filter. The filtering used by mp3 can exacerbate this problem and also cause peaks where
none existed before. The best advice is, if you are converting to mp3, don't go too close
3. I don't know - I use LAME.
4. Look for a program called
Razor Lame - it came with my copy of lame_enc.dll when I downloaded it.
JRP Music - Audio Mastering and Restoration.