In T362754#9721850, @Wargo wrote:

Is it on your wiki or Wikimedia?
If your, you need to install Extension:JsonConfig and import also data from Commons or modify module to not use them or disable some of its features.

Thank you for clarification, it's totally my bad.

In T358582#9580393, @Bugreporter wrote:

See https://wikitech.wikimedia.org/wiki/Heterogeneous_deployment/Train_deploys for how Wikimedia deploy code weekly.

Issue solved, we are using our custom VisualEditor forked from the official VisualEditor extension, after upgrading it to v1.42.0-wmf.18, all the issues mentioned are gone.