There is a game setting, "iWorkshopSettlerPopulationMax", that was the target of many early mods that tried to increase settler counts by "simple means" (i.e. without script edits). Eventually though, people understood that this setting has no effect whatsoever on a workshop's allowed population limit, and it sort of fell into oblivion.
Though, what most users still don't know is that this setting is checked (at engine level) by the code that brings up the settlement selection menu. To put it short, if a workshop's population exceeds the value of iWorkshopSettlerPopulationMax, sending a settler to that workshop or even linking up a supply line is no longer possible, and the workshop will no longer appear as a menu option (or is grayed out).
Thus, mods that increase the population limit should make sure to also increase the value of iWorkshopSettlerPopulationMax to match the maximum possible population. Might be worth checking with xEdit whether the mod of your choice forgot this.