Even though mods are identical, joining a game fails when mod settings have been altered through the ingame GUI.
Manually transferring the mod-settings.json solves the issue and players are able to join.

Looks like this related issue from bobs, as there are several conditional require statements throughout the mod:
https://forums.factorio.com/viewtopic.php?t=47020

Mods mismatch detected!
MomoTweak: Mod contents are different even though versions are the same. The most common cause of this is improper Mod Setting usage (conditionally requiring files based on mod settings). This can also be caused by modifying a mod files on the client or server but not the other.

This is very hard to solve for me cause I don't have a second machine to run another copy of Factorio
maybe I will look into it soon

According to Bob this is caused by the conditional includes and an easy way to fix that would be to move conditional INTO the file being included. I can create a PR for you on your GitHub if you want. Whatever is easier for you.

There are refactor branch that i already working on it, it may take some time to test and released a new version with better code

I see you have put in the suggested changes. Thank You for taking the time!
I will let you know if the issue shows up again.