Definitely the device tree, but each device tree is used by a driver in the kernel. If simply changing the data were enough, then the driver would not need change. I know nothing about your particular LVDS display, but Toradex does have some support for LVDS. If Toradex provides a driver which will work for your display, then it would be a matter of experimenting with the parameters the driver sees…some of which are passed on the command line, and others which are passed via device tree (well, a device tree is sort of passed on command line, but it is through a standard mechanism…eventually it all gets passed to the driver and it is up to the driver if or how to use the tree or other command line parameters).
Each LVDS will have different valid clocks and timings. I would expect this is a starting point. The layout of the hardware which corresponds to the wiring of the LVDS is another point…this often has its main dependency from the carrier board. Carrier board support packages include this. Once that is in, then you can possibly tune existing drivers which Toradex would have included. I couldn’t tell you anything specific about any particular LVDS, they are all custom and without standardization (some wiring would be the same among them, but timings are not standardized).