This does not seem to help,
lombok.var is still recognized as a normal import.
These two preferences were set to warn by default, but importing lombok.var produces no warning.
Setting them to ignore has no effect.

Is there maybe a way to enforce these settings in the JDTLS config itself, or maybe the command args?

I'm not aware of a language feature that would "unimport" something. This is not a JDTLS issue, neither it can be mitigated by configuring JDTLS or Java for that matter. This is a language issue.

Is this a Java 8 project? If so, use Java 8 or somehow configure your workspace source level compatibility to Java 8.

I don't see how this could work with something other than Java 8 (presuming I'm correct about var being included in Java 10, but even then Java 9 is not supported anymore).

Or do the sane thing: do not use wildcards.

It is a Java 25 project.
It is not really a language issue, since compiling the project works (and importing lombok.var manually causes a compile error).
It's that JDTLS resolution differs from the compiler.

I noticed that other editors' language servers have no issues with this (ex. IntelliJ), so I was just wondering if the fix for this has reached JDTLS yet. But it seems it hasn't.

TBH I'm a bit confused by that. Maybe you need to check the changelogs and bugs for JDTLS.