Not all HandledScreens are recipe GUIs, for example Blabber's dialogue screen :

I looked around but it seems there is no official way of disabling the overlay on specific screens, could one be added if that is indeed the case ?

This has been something I've wanted to support but I have to ask, why are you using a HandledScreen when you're not using slots?

Dialogues are controlled from the server, therefore I want to open it from the ServerPlayerEntity, know when a player closes the screen, have somewhere to store the state while the screen is opened, etc. Extending HandledScreen is the most straightforward way that I am aware of ¯\_(ツ)_/¯

Waystones and Tetra's crafting table and toolbelt for some examples of where blacklisting mod screens would be useful. Or at least a way to move the search bar besides bottom right and center.

(Incredible mod btw! I hope one day AE2 supports Craftables like Tom's Simple Storage Network, Crafting Station and others do. It's such a cool feature I've wanted in JEI for a long time)

This was fixed in 1.1.0, screens without slots no longer render in EMI.

Could you please add a configuration option to accept a list of screen class names under which EMI will not render? Certain mods do funky stuff with their screens and containers whilst having slots; it would be nice for pack development to have these screens display without EMI.