So I tried to fix the desync issue last night, but a bug in 0.15.9 is preventing me from testing multiplayer properly.
Rseding does not have access to a linux machine, so he is unable to reproduce the problem, but he believes it has been fixed for 0.15.10.
https://forums.factorio.com/viewtopic.php?f=7&t=46830&p=269748#p269748
I believe I have fixed the desync issue, but until I can test multiplayer, I can't know for sure.
Hopefully 0.15.10 will be out soon, then I can test and release a fixed version.