The option for disabling Shells in The End is not limited to this dimension. It disables shells in all dimensions with negative ids. Since Galacticraft uses negative dimension ids by default i had to change set I:allowCrossDimensional = 2 although i don't want to allow the potentialy bugged sync to The End.

I just took a glimpse at the code and i think the lines that have to be changed are just 98 and 405 of
https://github.com/iChun/Sync/blob/master/src/main/java/sync/common/core/EventHandler.java .

But since im not willing to set up a complete IDE for Minecraft right now I'm not capable of implementing a fix by myself. I would appreciate it though if someone with a working modding enviroment could look into this.

I've had a different experience than you. For me, that config didn't help compatibility with Galacticraft. I'll explain how it works on my server with updated versions of both mods.

Once I load another dimension (moon/mars), the server seems to know about them and populate the Sync list with shells in those dimensions. Even if I don't load the appropriate chunks.

Once this happens, then I need to relog with my client. I imagine the server is sending the client the updated list.

After a server reboot though, the server forget about those other dimensions. I need to manually load them and relog with my client to get them working in Sync again. I've taken to simply logging off on the moon so I don't need to do this constantly. /dimensiontp in Galacticraft lets you warp between dimensions so you don't need to take a rocket every time at least.

The End is dimension 1 (positive) and Galacticraft uses negative dimensions, so I don't think that's where the problem is. Even putting chunkloaders on other dimensions doesn't seem to fix it though. It's like the server doesn't know about them until you go there yourself.