FreeCad’s FEM capabilities are not really up to the task mentioned. But you can use it to get the .step files, which is the exchange format and I’d imagine that any tool capable of importing OBD++ should easily import .step files. You’d probably need to set the parameters of different items (copper, substrate, mylar, …)
Currently the fcad_pcb macro which imports KiCad layout to FreeCad does not support board stackup (which is available in 5.99). But the author is quite responsive so maybe you could ask him/her to support importing the board stackup.