Is that how it's supposed to work? It seems odd.
Kind of? Yes?
What happens here is that when you hit Q on Illithids, all components are set to be skipped (not asked about) and processing for the Illithids component itself is halted and WeiDU proceeds to the next component. If a temporarily uninstalled as-of-yet unprocessed component is set to be skipped, the stack manager automatically selects installation ("I") and proceeds to the next component. Once every component has been processed, WeiDU reinstalls any temporarily uninstalled components. These end up after the ordinarily installed components. This is why Illithids is reinstalled last. If you wish to preserve your installation order, you need to select "N" or "R" for all the temporarily uninstalled componets. The command line is probably more convenient for stack operations (for instance, you can use --reinstall to reinstall all installed components).
Incidentally, are you sure 'test' remains the last component after you have done this? I would have expected it to be reinstalled before the other mod, last of the SCS components (or before Illithids, with the Q thing).