When running /lp import permsexport, I get the following output:

[LP] Error: File /home/server/ms3/4.1.1/./luckperms/permsexport does not exist.

It appears LP determines the path from the server root to the config directory is ./luckperms/, not config/luckperms/.

SpongeAPI: 7.1.0-SNAPSHOT-43d8496
SpongeForge: 1.12.2-2705-7.1.0-BETA-3136
Forge: 14.23.4.2705
LuckPerms: 4.2.19

Bit confused

https://github.com/lucko/LuckPerms/blob/8cf0f7da5fc9382669d66ce65544eb41457aca52/sponge/src/main/java/me/lucko/luckperms/sponge/LPSpongeBootstrap.java#L244

(it's meant to target /luckperms/, but not ./luckperms/ as in the error you posted

Does Sponge's @Inject @ConfigDir(sharedRoot = false) on a field work correctly? I don't know how that internally determines the right directory, but it seems to point to config/<plugin>/ from my experience.

Yes it does, but LP data isn't stored there.

That's a misunderstanding on my part, then, though I agree the ./ doesn't make sense.

Just got a chance to look a bit deeper into this issue.

Seems to be a SpongeForge bug - can't reproduce this on SV - so will submit a fix there.