If set up properly, there is no reason why EoIP shouldn't work across a NAT, as EoIP looks like GRE from outside.
If EoIP doesn't work, you can use L2TP with BCP for L2 tunneling instead - since you have EoIP, I guess you have a Mikrotik at both ends.
Show the complete configuration exports from both ends. See my signature below for a hint how to obfuscate the sensitve infomration without breaking the internal dependencies between addresses, in your case it is very important.
Instead of writing novels, post /export hide-sensitive. Use find&replace in your favourite text editor to systematically replace all occurrences of each public IP address potentially identifying you by a distinctive pattern such as my.public.ip.1.