Load order does not matter. If it does not work for you, then you have a mod that is overwriting it.
If you do not know what mod it is, then you'd need to either:
1) Analyze your playset with Irony Mod manager and see what overwrites common/defines COMMAND_LIMIT_MAX
2) or use a text editor capable (notepad++, vscode) to search through your workshop\content\281990 folder for COMMAND_LIMIT_MAX.
If I had the filename of the offending file, I could make this mod be loaded after it.

The command limit max constant and most of Stellaris is loaded by alphabetical order and the last file gets loaded.

Is this actually working on 4.0? I just tested and It doesn't seems to work... does the load order matter? I have it near the bottom