Hello, I am doing something similar, the simulation in xschem and the one in Magic theoretically have to work well but in magic there are many details from the thickness of the wiring the way to put the labels the way the cables cross, sometimes parasitic capacities are generated after the LVS there is one last test that must be done: the extraction of parasitic capabilities is carried out and at the end a Post-layout simulation Create a test harness around the netlist with parasitic which is a .sp file
<http://web02.gonzaga.edu/faculty/talarico/vlsi/13_magic_inverter_sky130.pdf> In that document the procedure is explained, I hope it helps you