Run the command on the save file (you did back it up, right?)
inject_box_slots.cmd
(select 17-64 pages, 30 pals per page)
Start the server back up
And that's it, you can skip the rest of the listed steps in the tool pages, why?
Just running the tool against your save file, you will be able to see and interact with the additional storage in the Pal and Black Market merchant "sell pal" screen.
The extra steps that are listed in the tool's page (UE4SS, injector, download and install the "Bigger and Better Palbox" mod on the server and for each client, etc will only do two things if you get them all to work:
The extra slots (pages 17+) will be visible in the PalBox
New players will automatically have their save data adjusted to give them the extra slots.
If you just want the extra storage with the caveat that it can only be seen, reorganized and pals on pages 17+ moved to pages 1-16 at a pal or black market merchant, then you only need my 5 steps above and it only needs to be done once on the server (and again if any new players join to give them the extra slots).
No additional mods needed and the players connecting to the server won't have to do anything else.
I submitted a request in the official PocketPair PalWorld discord "ideas-and-wishes" channel to implement the UI from the pal vendors (when selling) in the Condenser. If they implement that idea, then with just the modified save file you would be able to condense the pals you have on pages 17-64 without visiting a Pal Merchant to move them to pages 1-16 first.
There's been a lot of advice for Linux Dedicated Servers saying the servers cannot run mods. I wanted to clarify with the above that you can run some mods without resorting to running the Windows Server via Proton/Wine.
UNTESTED But Should Work (not sure if client, client & server, or server only install