Enabling just "Add Secondary Structure" Structure preference when importing structure via CLI results in temperature factor being shown in alignment

The structure preferences are not being correctly interpreted by the new CLI mechanism.

If just the 'Add Secondary Structure' preference is enabled, and a structure added to a sequence via CLI:

~/Applications/Jalview.app/Contents/MacOS/jalview --open=examples/test_fab41.result/test_fab41.a3m --structure examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb --paematrix examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json

The alignment shows the temperature factor, but not the secondary structure - which is not what the preferences suggest should happen.

Enabling both 'Add' options result in both annotation tracks (correct), but disabling 'Add Temperature Factor' results in no tracks being added.