You can’t have a 1000 sat channel. There wouldn’t be enough in reserve to cover the on-chain closing fees. Millisats are mainly used for internal accounting, for things like routing fees between nodes. What gets sent in transactions are still full sats.

According to the LND repo on GitHub:

MilliSatoshi are the native unit of the Lightning Network. A milli-satoshi is simply 1/1000th of a satoshi. There are 1000 milli-satoshis in a single satoshi. Within the network, all HTLC payments are denominated in milli-satoshis. As milli-satoshis aren't deliverable on the native blockchain, before settling to broadcasting, the values are rounded down to the nearest satoshi.