I have worked out that Clear Terrain and Flattening are Construction jobs. Clear Sapling and Stumps are Forestry jobs. Just wanted to share that since it helps with the massive backlog of jobs.
I don't think one way is inherently better than the other. What matters is knowing which filter stops which jobs.
To be honest I think it is fine as it is, as in who does what out of those jobs. Makes sense for removing plants and saplings to come under forestry and terrain and flatten construction. I agree with Mikel though on his comment. It is true doesn't matter really which way it goes.
The one change I would make to these jobs is when they are auto generated by placing a building or a terrain segment getting flattened: create one job with the objects to be removed as child tasks, rather than one job per object. The current way, if you build across a forest, will absorb multiple work crews to chop down individual trees, which causes any additional crew members to just idle. Admittedly this is suitably Bureaucratic, but it seems to just slow progress down and flood the jobs list.