In streams you at least somewhat familiar with (and often most other streams as well...) it usually isn't difficult to figure out the Commission's sectioning rationale. It is more often than not tied to utilization or how a given section of a stream is designated for fishery purposes (stocked or not, special regs, class A, etc.) or to major physical changes to the nature of the stream (an impoundment, junction of a large trib, etc.).
For example, you might have a stream that the PFBC has divided into five sections. Section 1 is unstocked water that does not meet Class a criteria. Section 2 is Class A for a mixed BT/ST population. Section 3 is stocked trout water and ends at the headwaters of an impoundment. Section 4 is stocked trout water from the dam downstream to a point where it is no longer considered suitable for trout stocking due to the junction of a large warmwater trib. Section 5 is from the end of the stocked water down to the mouth.
That's a lot of wind to make a couple of relatively simple points: Special reg areas are almost always their own section. Same with Class A sections. Other section limits are usually defined by the beginning or ending of stocking or significant physical changes to the stream such as dams, large tribs, etc.
I know this isn't the question you asked, but I don't know the answer to that one, so I thought I'd answer this one instead...
