Using a Z-1000 and Z controller to vary voltage through a TIU channel probably wouldn’t be a problem (except on FIXED1 if you are using that channel to power the TIU). I use postwar ZWs set at 18-20 volts to provide power to the TIU inputs. I mostly run DCS locos and have my VAR channels set at Fixed. When I run a conventional loco, I use the ZW throttles.
Its never caused a problem with the TIU, but in a few cases (a Williams and an RMT Beep), the loco wasn’t happy. For the Williams, I installed a jumper around the TIU channel. For the RMT, I found that running it with a lighted car made the loco happy.