There's no way out of that implausibility, because it starts when Minecraft allows you to store a source block of liquid - one cubic metre approximately - in a bucket. The 1000L is an inevitable consequence of that, because one cubic metre equals 1000L. You might as well start to complain that our Minecraft avatar can carry more than a thousand cubic metres of solid iron.
Well i kinda do
eventually there might come a complete realism minecraft overhaul mod/modpack for the extreme hardcore minded people that would see how you could potentially do stuff in real life. of course punching trees and such would be disabled, floating blocks is probably unavoidable tho. This would make railcraft shine so much more imo if you couldn't carry a whole industry in your backpack and you would get a different kind of satisfaction getting things done.
I see you want me to complain about how much the avatar can carry and i might, but the game is balanced around that and it could have been avoided by different game mechanics. The gregtech ore veins is an excellent start on this: With these veins you could setup a industry to gather the ore and have minecarts bring back the goodies to your base automatically for processing. But if ores get more difficult to acquire then maybe a cubic meter of iron ore should give more than 1 iron ingot? I'm not sure how efficient it is in real life but it might actually already be pretty spot on, but making a shovel head out of 1 cubic meter of iron ore doesn't seem realistic. There are other more extreme examples but minecraft simply isn't balanced around being realistic but that shouldn't stop us from trying.
The macerator gives you 2 Ingots out of 1iron ore so i think BC IC and GT authors all already have realized this a long time ago.
So at the first days in minecraft you will setup as base where you find the iron or coal or whatever you are looking for or happend to find, then as you progress you can setup a base were you want because of minecarts.
Things tend toward realism in the end but i guess i won't find it in minecraft at least, which is fine. The gameplay of minecraft is probably better than a complete simulation would give anyways.
I guess you like mB over L for some reason, i think mB look kinda nice, but it is one extra letter usually for calculations and its hard to fit that on signs and in clipboards etc. I would actually want a 1 sign solution to L/t as "L/t" is actually 3 symbols and seems redundant if we invent another 1 symbol term for it but it feels a bit farfetched so i'm good with L/t as it is at least 1 symbol less.
Why insist on using mB as a measurement tho? were did it come from originally , BC? IC? RC? and is it used internally maybe? i'm not sure about what forge prefers for liquids internally.
About the 1 symbol solution:
https://en.wikipedia.org/wiki/Volumetric_flow_rate
They usually use the symbol "Q" for volume over time. So 10Q would be 10L/t. Elegant solution right there and it is an official symbol and more compact and useful. Hope i'm not mistaken.