The first of these bugs has been fixed in the nightly build and v3.5 stable build version 1.12.10 released just now (see Update to v1.12.10 (Nightly and v3.5 stable releases) for further details)
An additional behaviour change is that the PMI Align to Inertial Principal Axes node will now modify the chirality in the returned MOL cells as RDKit now automatically percieves chirality from 3D coordinates where none is indicated.
Steve