There's actually a related problem also: If you delete a mod that was disabled, the world won't start anymore until you remove the "= false" line from world.mt.

One more potential nuisance: I know some people who rely on the engine pre-filling world.mt with load_mod_* = false entries to actually create, or initialize their world.mt file.

EDIT: could a possible solution be to only write the entries when the world.mt is created for the first time (world creation) then never update it anymore?

Personally, I'd love to see this implemented though!

the world won't start anymore until you remove the "= false" line from world.mt.

Huh? I can't get MT to care about disabled entries, if you meant enabled ones the world will still start up but throw an error:
2021-07-06 19:24:38: ERROR[Main]: The following mods could not be found: "asasasasas"

Related codes: https://github.com/minetest/minetest/blob/cec0dfcbbda1e11e5ff2f45e58ea393d0437d7c6/src/content/mods.cpp#L307-L310
Suggested solution (not tested yet):

diff --git a/src/content/mods.cpp b/src/content/mods.cpp
index 434004b29..22127d242 100644
--- a/src/content/mods.cpp
+++ b/src/content/mods.cpp
@@ -306,8 +306,6 @@ void ModConfiguration::addModsFromConfig(
                        const ModSpec &mod = *it;
                        if (load_mod_names.count(mod.name) != 0)
                                addon_mods.push_back(mod);
-                       else
-                               conf.setBool("load_mod_" + mod.name, false);
                }
        }
        conf.updateConfigFile(settings_path.c_str());

Huh? I can't get MT to care about disabled entries, if you meant enabled ones the world will still start up but throw an error:
2021-07-06 19:24:38: ERROR[Main]: The following mods could not be found: "asasasasas"

He means:

1. Create a mod called foobar
2. Let Minetest to auto-generate the world.mt with load_mod_foobar = false
3. Delete the load_mod_foobar = false line
4. Minetest won't load the world again (but it is false afaik and it will re-generate load_mod_foobar = false again)

One more potential nuisance: I know some people who rely on the engine pre-filling world.mt with load_mod_* = false entries to actually create, or initialize their world.mt file.

If we had a good MT cli for server management, this wouldn't really be needed

I will add that not just valid mods end up in this list. Every folder name that isn't a mod ends up in the list. Even empty folders.

And it clutters the file badly: #12691 didn't even notice he had player_backend twice in his world.mt file which caused him issues.

It took me almost all day to find this duplicate line. The server was down all the while.

I will add that not just valid mods end up in this list. Every folder name that isn't a mod ends up in the list. Even empty folders.

Are you implying it's a privacy issue? I doubt most would agree.

Montandalar who made this issue said so and he only thought of mod name fingerprints. Just scroll to the top of the page and read it again.

I share his opinion. I often move stuff there during development that aren't real mods. I wouldn't have guessed all those folder names get shoved into every world.mt of every world I load up.

If I shared those, they'd see my entire .minetest/mods folder.