Thanks for the post. I just checked the code (vinaWizard.py); it does creates conf.txt from scratch and it doesn't reuse an old config file. For AutoDock 4, PyRx reads old input files and resets grid dimensions. For Vina this can be readily implemented as well. I'll be happy to help if anyone is interested in doing that.
Please Register at https://sourceforge.net/user/registration and send me your Username. I'll add you to PyRx team that would allow you to make changes to the code. I assume that you can code Python and can setup Python development environment. If not, I can direct you to online training materials, if you are interested.