Turns out its a problem that is independent of windeployqt or qtcharts. Will be logging my findings here in case anyone else comes across this specific-ish issue as well. (Or if anyone has other insights)
The qml files with the charts being loaded in use singletons. I registered these singletons in the c++ main. When I registered the singletons I have the code looking into the working directory for the singleton qml files using the QDir::currentPath() function.
The folder including all the singletons must be included in the same folder as the exe for the app to have access to these files. Dropping the folder with the singleton qml files into the same folder as the exe fixes the problem.