Started with the stock altitude of the airport and made sure the Afcad matched it. I then made a flatten covering the entire airport at the same altitude (I had some bigger buildings floating on the east side of the airport). Finally decompiled KLAX_rw.BGL and made some changes there. Removed the displaced threshold markers from the file (replaced by more accurately placed markers of the Afcad, this probably changes the runway lights, but I can live with that). And I changed the altitude as well. Same slew from KFAT shows no more bleeding, I'll try to do a regular flight later.
Figuring this out has given me renewed insight into the scasm runway files used by many devs, I'll now go fix a similar issue with the ImagineSim KEWR scenery, which was brought to the attention of the dev, but never addressed.
Should anyone want any of my files, send me a PM.