Bulk Renamer unexpectedly/wrongly stays on top of Thunar if you click Thunar from the panel, but other programs go on top of BR as expected.
Actually this is expected, every dialog stays on top of its parent window. It happens that some are modal (e.g. Rename File/Folder, Select by Pattern, Configure Columns and About) while others aren't (File/Folder Properties, Preferences and Bulk Renamer). The rationale is that dialogs don't get window button on panel, so if their parent window could put them down, the user would easily lose open dialogs in the stack of open windows.