Because it means that he's used the entire balance, sending a lower value (3 decimal places lower) than his intended amount should produce change.
With change, the second warning shouldn't appear.
Let's say that he's intended to send 0.01BTC but typed (0.01mBTC) 0.00001BTC instead,
if he got a single UTXO that can cover his intended amount (higher than 0.01BTC), using it as input in that txn will create a change so the second warning shouldn't appear.
if he got multiple UTXO that can cover his intended amount, only the ones needed to pay 0.00001BTC are spent leaving some available UTXO so the second warning shouldn't appear either.
The chance that it's the case is if the input's excess amount is used as fee which is "15.61% of the amount" sent.
Maybe in specific cases where the owner thinks that his 'N mBTC' displayed balance is 'N BTC' and didn't sent a very small amount which otherwise would show higher than 15%.
But it wouldn't hurt to replace it with a more specific message
Maybe a shorter version of yours, like adding "..without deducing the recipient's amount" to the original message. (still long though)
You may consider making a 'Pull Request' that edits the warning into something similar to the example, if the core developers think it's necessary, they will merge it.
If not, they would post a reply regarding the reason why.
The part to edit is currently in this line: github.com/spesmilo/electrum/blob/83e14794a1e1202ecfd40f0ea779f0b91ccf2032/electrum/gui/qt/confirm_tx_dialog.py#L579