This setting affects auto filling (bot_autofill). The server will try to keep 1-2 free slots to allow players to join if it is enabled. It will automatically kick bots to achieve this.
bot_keepfreeslots kicks just one bot if the server is full but it also tries to keep the game balanced. So if kicking one bot leads to an imbalanced game it may also kick another one to keep the team sizes equal. This leads to the fact that this command may keep 1 or 2 player slots free.
Note: bot_keepfreeslots has no effect unless bot_autofill is enabled
Attention: bot_keepfreeslots does not affect bot_count