What are the main geological processes that can cause local biases in the fossil record, e.g. when comparing species diversity or species occurances in different areas from the same time period? I know that there exists several processes for fossilisation, and that local environmental conditions are essential for fossilisation (e.g. to allow for rapid burial/sedimentation). However, my question is dealing with processes that affect a fossil record that is already formed (i.e. the period from after formation to present time). I realize that local conditions affecting the formation of fossils is probably the main reason for local biases, but am curious about processes affecting the later stages of preservation.
I have studied archaeology, not paleonthology nor geology, so most of my answer is either extrapolation of what applies on younger material or layman's five cents. Still I hope it will be useful somehow.
You already mentioned the fossilization processes - this is bit distant from my field so I'm glad that you are not asking for details on them. In archaeological record, organic material can survive for centuries only under specific condition, often similar to those leading to fossilization. These conditions are one of the main factors contributing to the density of remains of ancient people and the animals and plants accompanying them, along with past human behavior.
Inhumation helps to preserve the bones, or, with specific grave construction and acidic soil, hair and even soft tissues (Egtved girl is a famous example). Anyway, animals or even plants never practiced any ceremonial burials, so this behavioral aspect is marginal for ancient fossils. Just that organisms whose habitat was more prone to fossilization are preserved more often - but this is still part of deposition and fossilization stage.
Excluding the fossilization processes (which are crucial), geological stability is the factor number one (or number two, after them). The more volcanic activity, earthquake and/or erosion, the higher chance the fossils will be destroyed. As an archeologist, I had to learn at least a little on erosion, because they can destroy the artifacts we would like to find, or at least move them so that we might be confused in evaluating the context; I believe this applies even more for the millions of years of the fossils' lifespan. If I'm right (I might be wrong; this is not my field), this is not as important as the conditions for fossilization, because the erosion and other processes that might destroy or degrade the fossils are spread more evenly than the good conditions for fossilization.