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I'm pretty sure a discussion about furnace prototype input slots has occured before (I just couldn't find it) but here I'm requesting that furnace prototypes have more than 1 input slot. Currently, the only alternative is to make a storage entity and perform a lot of complex control scripting to simulate a furnace prototype with more than 1 input, which can lead to desyncs if not done correctly. Another issue with that is that the "input" and "output" slots are in the same inventory meaning that whoever is playing the mod has to do circuit network logic in order to use the machine. Note that using a regular crafting machine prototype isn't always an option, especially when there's a lot of recipes which that machine can do. (picking between, say, 4095² recipes isn't going to be fun for anyone)
The simplest solution (in my mind) would be to force recipes in that furnace to contain the same amount of ingredients as the furnace can hold, meaning that, for instance, a furnace with 2 slots could only have recipes with 2 ingredients. A better solution would be to allow recipes in that furnace to contain less ingredients than the furnace can hold, but that might be quite complicated, especially when 2 or more recipes (1 which requires 1 item, another which requires that same item and another one, etc.) are available in that furnace at once. In that scenario I'd suggest picking the recipe with the most inputs possible or assuming that the recipes with less inputs also require (but don't consume) an empty slot.

If there was some reason why this wasn't made possible previously, please share it with me.

An example of where this could be applied is the mod shapeztorio which implements the control logic solution in their swap box "machine", which as in the description is actually a container prototype with added control scripting. Right now, the "Rotate 180 + stack" and "Rotate 90CW + stack" machines are furnace prototypes with 1 slot, which were created to get around the limitation of having at most 1 input slot on a furnace prototype without more control scripting - instead of doing the stack operation independently of rotation, it takes in 2 of the same item, rotates 1 of them and then stacks it. (but it doesn't work right now, I don't know why - that's just the intent)
The 4095² example was actually from this mod, because each input (in the stacker) can be any one of 4095 items to create a valid recipe. (this is why `for` loops are my friend)