Set up a two process print, one model with raft and one straight on the bed. it tries to print the entire raft first and then drop Z back down to the bed to start the first layer of the non-raft model. Not sure why it wouldn't alternate layers as with the rest of the print. but anyway, that will work as I oriented the parts so the nozzles wouldn't hit.
The raft and skirt for the raft print fine at the expected first layer height. However, the non raft part the Z height is wrong and the first layer tries to start at about 0.00Z.
I suspect its just a bad idea to have raft and non raft parts together but interested to see if anything can be adjusted or if it's just an issue. factory file attached. Thanks.