The semantic JavaScript highlighting overrides token color customizations. The overwrite works like a mask, so if a range is not covered by a Semantic Token, the TM token is used instead.

Currently, there is no way to resolve this except for turning off semantic highlighting for a current workspace, or for all themes that are being used.

"editor.semanticHighlighting.enabled": false

We can document this limitation as a first step and consider creating our own MongoDB theme in future iterations.