Thanks so much for this post. If you are getting drastically different numbers between --scf and --scfl it could be due to a bug in the scfl calculations.
If you could open a GitHub Issue (https://github.com/iqtree/iqtree2/issues
) for this case, and share your alignment, ML tree, log files from the ML tree analysis, and input files (either on the issue, or us a link via email if you prefer not to upload them), we'd be really grateful.
There's a chance that this is a genuine difference between what likelihood says and what parsimony says too. But from the other info you've given, a bug is certainly high on the list of possible answers!