Semantic Token Inconsistencies between Editors

### Describe the Bug

I am noticing some bugs around semantic tokens in neovim. Below is a screenshot of some code I am working on (code attached as well for reference)

On the left is vscode, running pyrefly 0.45.1 and on the right is neovim running pyrefly 0.45.1.

You can see that the semantic tokens in vscode all seem to be applying correctly but in neovim they aren't, The one that caught my eye is the coloring for "MetadataManager", a custom class I am writing

Interestingly, pyrefly _is_ applying semantic tokens for _some_ stuff in Neovim, exceptions for example are being correctly highlighted

I have noticed lots of weirdness around semantic tokens lately but I finally decided to submit something to see if I am doing something wrong here.
I am not sure how to "inspect" the highlighting of a token in vscode (or if that is even possible).

In neovim, I am using neovim's native `lsp` and my command is simply `pyrefly lsp`. Currently I am passing no options along to the lsp server.
I also attached the log from neovim's lsp client, maybe that is useful? Please let me know if there is anything else I can provide!

[test_manager.py](https://github.com/user-attachments/files/24088374/test_manager.py)

[pyrefly.log](https://github.com/user-attachments/files/24088376/pyrefly.log)

### Sandbox Link

_No response_

### (Only applicable for extension issues) IDE Information

_No response_