Currently, in GPlates, the raster must be a present-day raster in that the raster data must represent present-day positions. The raster can also be time-dependent but the data in each time slice is still expected to represent present-day positions (ie, be in the plate reference frame where the plates don’t move/reconstruct through time) - GPlates will then reconstruct the plates and the raster data will follow the plate motion.
To reconstruct a raster representing data at non-zero times you can use gplately with a non-zero time in the Raster object (see here). There’s also a Notebook covering rasters here.