Looking at how modding is documented and implemented, it would appear as though there can only be one mod at a time which modifies any given data file. That is, if two mods modifying policies (for example) are activated at the same time, the one last in the load order will be the only one which actually gets modeled in the game. Is this the case, or is there something happening under the hood which allows multiple mods at once?
Multiple mods can change the same file because what happens is that each line in the modified file gets appended to the end of the file. I’ve just checked this locally to confirm and not only can multiple mods run simultaneously but modded policies can influence the simulation objects that other mods create. I don’t see there being major issues with mod compatibility.
That being said mods that change the prereqs.txt file will (probably?) need to have a unique number for each prereq and mods that add countries might need to have a comparability mod made for them to have your defined prereqs set properly (ex. if you add _prereq_has_canal and someone else makes a Panama mod you might need a third mod to tell Panama that _prereq_has_canal should be true)