I've received this Muluna bug report that you should take a look at and address. Your mod changes fluidboxes in the foundry in a way that breaks recipes with more than one fluid product.

https://github.com/nicholasgower/planet-muluna/issues/460

I Have also seen this be a problem in mods like Pink's metallurgy where tungsten pipes will not connect to the foundry so you can't use lava at all making it impossible to progress. I think this is caused by the same bug.

Hi,
Thanks for the report.

This is a known issue. Unfortunately, there is no general solution to the problem, at least for the moment. I have to manually edit recipes that have multiple fluids as inputs or outputs and do not specify the index for each one. This is due to the way the game automatically assigns fluid_boxes to recipes.
https://forums.factorio.com/viewtopic.php?t=135663

I plan to make this manual adjustment for the most commonly used mods and those that people ask me to.
In the meantime, I’ll create a setting to disable this part of the mod if necessary.

I think you could make the process automatic if you run a for loop on every recipe of the relevant categories. Muluna does something similar with assembling machine recipes that use fluids to make data fluids usable on assembling machines. https://github.com/nicholasgower/planet-muluna/blob/73713505aac6b7f7d7340ed5e073e2d9a11d298b/prototypes/final-fixes/data-cells.lua#L9 Feel free to draw inspiration from this.

Is there a reason why you need overlapping fluidbox inputs? Why can't you just use the already existing fluidbox inputs?

I've writen to you on Discord ;)

In version 2.5.0 I've added a setting to disable this part of the mod if there is a compatibility issue.