I can see a very distinct reason for wanting to be able to modify the LyX- generated preamble directly (without having to use a separate editor). I'm using MathTime Professional II fonts and I want to use it in conjunction with the bm package so that I have access to the bm versions of the \bm and \hm modifiers. In order for this to work, \usepackage{bm} _must_follow_ \usepackage{mtpro2} and with LyX generating \usepackae{bm} in its own preamble, the second \usepackage{bm} in my preamble is rendered useless. I see this as much more of a hindrance than a feature.