Never faced that issue. I integrate all updates for Office 2016 volume version with WHD after converted them to msp files and recreate the iso for french X86 and X64 and English US X86 and X64. After installation I use latest MTK which is updated and followed by @abbodi1406 now. Tests I've done some days ago are ok. Office is running perfectly. To get updates remember in update options (Windows 10) to set ON "Receive updates for other Microsoft products when you update Windows". That's all.
How do you do to convert it to msp? Also what's MTK? I tried these Office 2016 VL but didn't receive any updates offered by WU, I also downloaded the updates by using WHD but it says "No Office installed bla bla".
MTK has got a revival by @abbodi1406 https://forums.mydigitallife.net/threads/microsoft-toolkit-continued.82782/