I'll try to answer your questions in order:
1. I can hear a difference between rosewood and mahogany even with laminated back and sides. The rosewood has a much fuller sound. In my non-scientific survey of professional acoustic guitarists I've come across, about 80% of them us rosewood back and sides.
2. In my experience with 6 string acoustic electric guitars, the built in electronics had no effect on the acoustic sound IMHO.
3. The LR Baggs Lyric or Anthem systems sound amazing. Heather Maloney uses an LR Baggs Anthem system in her BR-60T. Search Youtube to see what it sounds like.
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