Not quite sure how the start up setting works but if i try to add in the prototype manually it crashes on start up when adding in a bot type.

Hello,

I outlined here how you can change the capsules it throws ("consumes") and bots it deploys:
https://mods.factorio.com/mod/Auto_Deploy_Destroyers/discussion/673509c12c18d10d9b02763e

If you can tell me which modded bots you would like to throw, i can take a look how those are technically named in the backend.
Those values should be entered in the settings.
Specifically the name of the item (capsules) and name of the entity (bot).

I can think about adding another armor equipment for "Modded bots", with perhaps a nice in-game menu item to select the relevant capsules.
But if they are significantly stronger for example, my deploy rate calculation might also need tweaking.
Will put it on the backlog for when i have time.

Its for Apia-Carnovas 'Flamethrower Drone' and the standalone 'Tesla Destroyer Robot' from mod of the same name

Hello,

https://mods.factorio.com/mod/TeslaDestroyerRobot
item name: tesla-destroyer-capsule
entity name: tesla-destroyer
entities per capsule: 5

https://mods.factorio.com/mod/apia
item name: flamethrower-capsule
entity name: flamethrower
entities per capsule: 1

If you've reached the stage of the game where you have access to Tesla tech and other planets, i assume you won't be needing Distractors or Defenders as much, so you can try to repurpose those launchers for other bot types.
Keep in mind that the deploy count calculation for Defenders and Destroyers is the same, but Distractors launches a significantly smaller amount of capsules.

You may also need to tweak the number of bots deployed per capsule, to match the current mods.
Those are in my mods settings in category "Map"; "Entity deploy per capsule for ..."

If you find it deploys way too many/little bots overall, you can also try updating my mods setting for "Aggression Factor". Default is 1, lower to deploy less bots and increase to deploy more bots.

A fair warning, when i had around 150 flamethrower follower bots, my FPS/UPS tanked to the single digits :P.
In that case i recommend replacing the Distractor launcher to be the Flamethrower bot launcher.

Let me know what works out for you.