There are a number of reasons why:
1) Reduced QA.. the fewer tweakable parameters, the less testing of combinations is needed per revision.
2) Support issues. Many BIOS options assume a fairly savvy user. Motherboards targetted at entry level users are easier to support if they don't assume someone's 14-year old didn't find a "Clock the CPU to 20000mhz D00D!" on an AOL forum, and tried it.
3) Costs. Some times lesser-end components can be substituted for reference components, but with lower tolerances. i.e. say a particular BIOS setting, if used to it's highest value, requires a certain level of capacitors.. but the manufacturer found it can cut costs by using lesser series..
There are many, many more but these are the most common reasons for limited or hidden BIOS support.