Messy office freaks me out

It took a long time to (mostly) train out my wife's tendency to move things around on my desk and work-surfaces.  When I have to repeatedly spend minutes trying to find the paper-clips, the checkbook, or the utility bills I was about to pay  -- all of which were, that morning, within reach in two seconds -- it drains my willingness to actually maintain or progress the household.  And I say so.  Eventually it sank in, like after I pointed out we had to cancel yet another highly-anticipated trip so we could pay the late fees on bills which were moved out from where I could find them to pay them ....

Every other open-office job I had in my career, I have had the same issue.  Folks would wander in and displace (even disappear or add) stuff.  I want to get work done, stop slowing me down by removing hard-to-find supplies, moving projects in flight, depositing heavy items which smear stains across the desk, leaving leftovers atop my phone for the ants to get into (!!), and taking equipment and hand-crafted gear!

I soon learned to clear my desk and lock away everything at the end of each work-day.  Every-last-thing.  Anything out on my desk or in my workspace when I arrived, was "top of the inbox" and got dealt with (often trashed) straight-away.  Yes, it made me look slower on the scale of a day -- yet I still "unbelievably" stayed a top-performer month-in and month-out.  Between the "Getting Things Done"-inspired sharp organizing, and the hard boundary of "start-of-day take out what's needed" and "end-of-day put everything away", I can cope with a lot of slop overflowed into my workspaces without going off-kilter.

My current work environment?  A one-person office in the basement at home, with window-blinds that shut and doors that *lock*, and household members who have been trained to keep that room undisturbed.  It's so out-of-the-way that it takes conscious and intentional effort to get to it -- does wonders for discouraging "hey just thought I'd drop in" or mindless poking-around.  I'm so much happier.  And I still run checklists to start and end each working day in that space.  Clean desk out, clean desk in, clean mind throughout.

In roles focused on efficiency, I took several steps, some of which you've already noted.

• locked up all supplies and workspaces at end of day
• checklist for start-of-day which includes cleaning
• alerted my bosses and project-managers which "wandering supplies" and "disappearing materials" caused which specific delays, with notations in my logbooks (copied to them weekly with monthly summaries) to track the effects in terms of time, cost, and stuff I could not do for them and others -- basically passing the heartache 'upstairs' when it's an obstacle beyond my ability to correct
• checklist for mid-day and end-of-day to walk my peers to see what I needed to deliver to them
• extra kleenex, paper, pens, post-its and similar "sacrificial" supplies just across from my cube/office entry
• lunches or coffees when I find someone "invading my workspace", to try to work out how to get them to stop doing that
• at one job, I had to involve Legal (beyond the usual 'how do I protect this from getting stolen' into 'how do we protect this from getting stolen again') as the materials going walk-about were particularly sensitive

It was far easier at home -- I could train the children (and eventually my wife) to respect others' space.  At work, there was always people cycling through (turn-over, cross-training, other teams when in high-traffic areas, ...) and always another few people who hadn't learned.

It sounds like your workspace is out around people, and you can't really control what other people do while you're gone. Working with other people means having to be flexible in ways that you don't want to be. If you know they'll mess things up when you leave, then lock up the things that you don't want taken/used/thrown around. If they have to access your folders, delegate the responsibility to one person -- a single person will feel more accountable than a group who can grab a file any time they want. Accept that things will just be that way when you come back, and embrace Marie Kondo's saying, "I love mess" -- because it feels so good to clean it up!