The way it works is by creating a fake client (fake client != bot) which is put into team 3 and ghost mode (or dead). When spawning a SI the ghost client will takeover the spawned SI. Thus, ignoring the VScript and Cvar spawning limit, since it only kicks bots over the limit not *fake* clients. After that you can just kick the fake client and a bot will takeover. Just like in versus if someone is in ghost mode and you spawn a SI, the player will takeover the spawned SI.
Pretty clever.
However z_spawn is bit broken, you may wanna switch to z_spawn_old to use <area> or <auto> arguments.
Alternatively, you can also remove the VScript SI limits which overrides the limit cvars.
https://forums.alliedmods.net/showthread.php?p=2535972