How do I analyse for, or what do I need to consider, when comparing gravity-opposed vs gravity assisted flow in a tube containing a porous bed that partially shrinks (through partial mass loss) over a fixed time period?
With gravity assisted flow, you have a higher potential of channel flow through the media, so sections of your plant packing won't be wetted by the solvent. Making sure you have the optimal flow pattern is one of the primary factors in packed column performance. You indicated a 10 to 15% volume drop in the plant matter, so this poses an issue that over time the solvent flow in will squish the plant matter against one end of the container; the magnitude of this problem will depend on when the extraction of the molecules you want takes place. It's also possible that you could fluidize this plant material after the volume starts to decrease. Fluidizing could be beneficial to get high surface area but you have to control it to avoid the bed compaction effect mentioned above.
The main thing to measure is the pressure drop through the column. Too low a pressure drop means you have channel flow and too high a pressure drop can indicate plant matter compaction. If you can use a clear container to hold the plant matter, you can tune your setup to keep the flow pattern you want - provided you can control inlet pressure of your solvent.