I recently discovered the same road/trail discrepancies between Topo 100k and Topo 24k in planning a primitive road dirt bike trip in SE Utah.
The 100k maps showed lots of roads not in the 24k set and vice versa. I found I had to really use both map sets to plan the trip. On one stretch I was kind of worried that the 24k map set showed a long road not going thru and there were no bailouts. I could see the road on Google Earth so we decided to ride it and it did go thru.