It seems default SCTransform subsamples 5000 cells (as specified by ncells=5000), and min_cells condition is applied on "the subsampled cells"–it checks whether a gene is expressed in at least in <min_cells> cells across the subsampled cells, whereas CreatSeuratObject checks the same thing across all cells, if I understand correctly. If one does not want to change the number of genes at SCTransform, min_cells=0 or ncells=<total number of cells in the object> would do.
