Note that I didn't cover accepting Lightning in this guide, but just add the following command in the "Configuring BTCPay Server" section to enable Lightning support via Core LN:
export BTCPAYGEN_LIGHTNING="clightning"
I'm happily accepting LN via my own custom Core LN node using charged to connect to it remotely:
export BTCPAYGEN_LIGHTNING="clightning"
charged
to connect to it remotely: