Paying 500 scrap at the farm is more bothersome than acquiring the scrap. I know that joke about it is even included in the 4th wall breaking dialogue, but adding 'hold key to keep adding', with increasing speed of depositing like how it is with trading depots would make it much more manageable (maybe even the code itself can be repurposed).
It is a joke and probably won't be change. If you press shift though it deposts 10 at a time (just like a trade output). Don't tell anyone :)