If you are developing the Game Engine yourself, I'd suggest you to use the OpenRaster ".ora" file format, and different layers to convey the needed information.
In the likes of LibreOffice's Open Document Format, OpenRaster is a specification to allow standardized exchange of rich-raster images, including multi-layer information. It is used by GIMP, Krita and MyPaint software to exchange images (and the later program even uses that as its native file format.)
Each OpenRaster file is a zipped directory containing a XML file with the digest description and one
.png file for each image layer - therefore you can convey an arbitrary number of dimensions in a single image file - all you need is to have your game engine to fetch the png files from within the zipped ".ora" container.
That said as a general advice, GIMP can easily allow you to modify any combinations of the R, G, B and Alpha channels: on upper half of the
(the second tab just after the layers dialog on the standard configuration, or
Windows->Dockable Dialogs->Channels to activate it from anywhere), just unselect the channels you want to protect from change.
By default, and almost all the time, the 3 or 4 channels are visible and selected. Click on them on this dialog to unselect them - for example, if you want to paste something to the Red channel exclusively, unselect the Green and Blue channels, make your paste as usual, them select them back to allow these other channels to be changed. These modifiers apply to all layers on the image at once.
Be aware that selecting and unselecting these channels is a distinct action from toggling their visibility - which happens by clicking on their "eye" icon.
(You can also create extra channels that are grayscale drawables, usually copy of selections - those will show on the bottom half of this dialog, and are an entirely different thing - don't bother with them)