Can you add blocks from other mods I play on a Minecraft server with mods (TNP Limitless 3) and there are more ores, I would like to use the auto miner with it, but I don't know if you can or not?

If you use #mine <name> baritone assumes you mean #mine minecraft:<name> and if the block is from a mod you simply have to use #mine <modId>:<name> instead.
E.g. #mine thermalfoundation:glass_alloy