Recently I tried to figure out how the kenney 3D assets works fine in Construct 3 and how to import the models keeping one single gradient color texture for all the models.
It's really simple, you just need to properly export the models by referring to the texture file in the export settings, be careful to not embed the file texture in the model file, otherwise you will end up having multiple copies of the same texture for every model.
I do this in Maya with a glTF exporter plugin:
github.com/matiascodesal/maya-glTF
And make sure to change the settings properties like this:
That's it! Hope this will be helpful and if you have a Blender alternative please share with us.