I can't believe no one brought up the obvious disadvantage of a pre-amp/power amp rack system! Having my own rack and going back an forth with many pre-amps and bass heads, I have figured this out.
Bass heads that have driver tubes before the power amp and heads that have all power tube sections CAN NOT BE REPLICATED EXACTLY with a pre/power amp setup in a rack. You can add gizmos and other units to try and get this effect, but you are never going to achieve the actual tone of what I just described. You CAN GET CLOSE to that sound, but from my experience, the head will always sound better over the pre/power amp setup. Even amps that are relatively clean sounding will sound even cleaner through a PA designed power amp. If you want a cleaner tone, this is the route to go. MOST bass heads have a "voiced" pre-amp AND power amp that allows the amp to achieve a unique tone.
4Mal - is absolutely right about Eden heads versus the Eden pre-amp, the Eden power sections are designed to give Eden amps a specific tone.
The GK Pre-amp versus the GK 700RB head - two different worlds of tone. The GK head has that punch in the midrange that makes bass tones just stick out in the mix, but going through the rack setup (QSC head), that punchy midrange was gone in favor of more low end and cleaner high end.
If you want really clean sounds and not much amp coloration - rack systems are the way to go. Otherwise, stick to heads.