The latest servicing stack update and the latest cumulative update solved the VT-d problem for us in 1803.
After the install and a reboot we could enable VT-d without any problem.
We also update a machine from 1709 to 1803 after KB4486996 and KB4485448 without deactivating VT-d with success.
So, for 1709 you need KB4486996 and KB4485448.
For 1803 you need KB4485449 and KB4487017