Is there a reason why rune pouches cap at 16k?

Late to the show unfortunately.

Its actually a bit of a complex issue. The reason its 16k is to do with how much data we can store on an object: when accounting for all the rune types, and up to 16k of each slots, that 'almost' maxes us out.

Now we could just swap that over to player data and have rune pouches read from that (this is what necropouch etc do, and why they 'share' inventories; because theyre just pulling that data from the player and showing you it)
and if we added a new thing today that is probably what we'd do unless we had a specific design reason.

However, the issue is a little deeper/more complex than 'just do it' because there's issues to consider like:
Do rune pouches still only have 4 slots? (then if they pull the same data your locked into 4 runes and need to manually swap each time you want a different 4)
If we do unlock it to above 4, then suddenly we have a huge surge of rune pouches people don't need as you no longer ever need more than 1; which would ultimately crash the price of RC thread.
And this is without considering small pouches etc. (though thats a minor thing)

the TLDR: essentially is we can change it, but it doesn't come without extra consideration/issues, and it's not as 'urgent' as other fixes in game (imo)

Ultimately I think the fix that kinda skirts round the issues is to have it just refill when you bank I don't think there's many times where you'll use all 16k before you bank... right?

i think preset loading or a 'always fill containers' toggle or something is the answer yeah