Obviously they _are_ real lightning payments, otherwise they wouldn't work with other wallets. It's just that Muun is an on-chain wallet so it uses Muun's server to send and receive lightning payments. I don't really mind this, I just hope they were more transparent about it. Also I don't think this model will scale well in the long term.
Discussion
Can you point to any documentation/articles that describe how Muun accomplishes it's submarine swap? Or do they keep it proprietary?