Are you using an old version of BTCPay? The newest version of BTCPay allows you to run your own lightning node and accept lightning, send, and open channels. 

Unless the BTCPay was not your server meaning you were not the administrator.  

 Yes exactly, I am not the owner of the BTCPay server, I use that of a trusted person. Unfortunately I do not have a public IP address and I could not use it on my Start9.