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When I use Evaluate Expression while debugging, Intellij doesn't take into account any enabled compiler plugins. Is this a misconfiguration on my end, or is there simply no way to use compiler plugins in Evaluate Expression?

To make it work you need to install/create IDE plugin for each compiler plugins, which will register those compiler pluings in compiler which is used in IDE for analysis and other tooling, including debugger

Also note that if your plugin is IR based, then it won't work in debugger, because evaluate expression still uses old JVM backend under the hood
Kotlin IDE team is working on IR based implementation for debugger and, I hope, it will be released soon

Are there any plans for IR-based plugins to be picked up automatically by the IDE then? Especially since with FIR the vision is to let the IDE automatically pick up on FIR plugins (and some of those plugins will depend on IR transformations). Evaluate Expressions working with plugins is obviously not vital to have but it is "nice"