How about a spell? or some other way to rename chests etc.
So we can have...Chest of scrolls, Chest of Armor, Chest of Dragon Bones etc etc etc.
or maybe put labels on them?
I go crazy trying to find where I've put stuff...just like IRL.

The only problem I see with this is that everything that has a unique name must have a unique ID. Otherwise you would change the name for all objects with that reference ID. In other words, renaming a chest found in your house will rename all other similar chests in the game. This is why finding the right house mod for you is important. Many house modders do just what you suggest - have differently labelled chests, etc. - BUT - each one has a unique ID that the modder created.

I'd suggest browsing the house mods to find one that sets up booty organization in a manner you like.

The best way to get around the issue right now is to use a quest alias with a unique "MESG" object as the name. Then you can change the MESG object to the name you want. This allows you to apply an alias to only one object reference without altering the name of all the objects with the same base reference. However, I think the hang up is in the actual UI. There is no way to actually input the name you want outside of the enchanting menu. Hopefully SKSE or SkyUI will provide a method for this at some point.

At last I found a home mod without cheats/merchants/npcs etc and with named storage/crafting/display space all in one room.

"Bert's Breezehome Cellar" on Nexus.

Check it out - he's a clever lad.