Indeed, it is a huge problem for science to define and keep a boundary with regard to metaphysics. If the line is drawn too firm, it leads to undesirable consequences of strong determinism. If it is drawn willy nilly, it leads to presumption and abuse.
Speaking of lines, there is a fine one between Intelligent Design and Theistic Evolution. I suspect that may be why ID is somewhat successful with parents and school boards.
ID has the potential of a much stronger argument than it has used so far. For instance, a measure of complexity was evidently developed and used by Dembski to speak of irreducible complexity. It was met with huge resistance. Yockey, on the other hand, used the widely accepted Shannon entropy to argue against abiogenesis. His views were taken seriously. Functional complexity was raised by Schützenberger. And other, non-ID scientists, are taking a hard look at the rise of autonomous self-organizing biological complexity through other methods, e.g. automata and Kolmogorov complexity/Solomonoff induction.
Even if they were to conclude that there is not enough time on the geological scale for the diversity of biological life to evolve in the order shown by the “tree of life” in the manner proposed by the theory of evolution - science will still want an explanation of the fossil record (tree,) and to get there, that explanation will of necessity point to the metaphysical.
That would open a floodgate of metaphysical explanations for phenomenon that science is loathe to entertain. Nevertheless, science is even now getting into the physics of consciousness and IMHO, will be compelled to move the metaphysical “line” at least somewhat.
For any Lurkers interested in more on my views of this subject: Evolution through the Back Door