A start on weed control would also be appropriate. In some places the rails themselves seem to be becoming overwhelmed by them, and it looks like something out of the third world. I can't believe that it "doesn't matter" because the roots must surely interfere with and ultimately block/break the drainage.
It damages the "resilience" of the ballast as well, due to the gaps between the stones getting filled up with humus so it all packs into a solid mass that behaves more as if the tracks were laid straight on the earth rather than on ballast, with deleterious effects on the track alignment.
I can't help wondering if a bit of applied botany might rewrite the rules, though I don't know enough about the vegetable kingdom to take the idea further... some kind of plant with the right sort of root system (thick tough woody roots rather than thin flexible ones?), along with the right sort of stone to suit it, so that the roots help to maintain, rather than damage, the resilience of the system, and at the same time unwanted plants find it difficult to compete. Scree slopes or recent lava flows might be the sort of place to look for suitable plants. If such plants exist it could be a largely self-maintaining system.
Some stations, particularly recently-constructed ones, can be very harsh and hostile places to wait for a train, especially on a hot day - great dry sterile hard glaring expanses of concrete and stone, like a scar of desert laid in a wound in the land. While plants growing in the ballast may be bad for the infrastructure, they do significantly soften the feel of such stations and make them more appealing places to wait; if "Bio-Ballast" did turn out to be a practical idea, it would be a win all round.