When using any Chest from SS (even the very basic one), I am not able to use any mod to insert items into an exact slot. (not trying to put upgrades or something like that)
Using ATM10 2.44 with SS core 1.3.32 and storage 1.4.25.
Tested mods: CC: Tweaked 1.115.1, IntegratedTunnels 1.8.37, Super Factory Manager 4.21.0.

For example will use ComputerCraft. I am able to export and read without any problems from all slots of the chest. When trying to insert items, they always default into slot 1, using any of the mentioned mods. I have searched the issues if there was anything related to this, however, I haven't found anything. I suspect that due to the complexity of your chests, you handle inputting items differently, which breaks this mod interaction.

To reproduce best with SFM. Chest - SFM controller - Chest. Code: input from a; output to b slots 5. Using vanilla chest, it is possible. Using SS chest, it will default to the first available slot.

This is actually an intended functionality - inserted stacks are stacked with matching existing ones / matching memorized slots / matching compression slots and only if all this fails they are inserted into empty slots starting from the beginning. This actually improves performance significantly as long as the inventory isn't completely full. In theory I could make a change that if it tries to insert into empty slot it will try to insert into the one that was passed in (if it actually is empty), but then again if the matching stack was inserted into a different slot it will try to first stack it with the one that already exists in the inventory so that would produce predictable results only for stacks that don't have a match in any other slot.

What is it that you are trying to achieve with inserting into specific slots actually? I would think that memorized slots should be perfect for organization of inventory slots.

Well, I was trying to automate Hostile Neural Netwrorks and wanted to have a large chest with one slot per each prediction where it will fill up to let's say 512 (by using stack upgrade). Additionally, I wanted to have in the same chest for generalised prediction, which would be using the void upgrade. I wanted to use only one SIM chamber with a CC computer to manipulate what needs to be crafted by inserting models from one larger chest.

I changed the approach and just made a simulation chamber for each model and just SFM to mass transfer items between all of it. But I sometimes use CC to automate more complex stuff, namely things in Botania come to mind. But with your explanation, it probably makes sense not to touch this stuff and maybe keep it as it is or could put a toggle inside the chest settings, however, I feel like that is too much customizability and probably isn't the best design? You the author.

BTW just note on Hostile Neural Networks, the models and predictions use NBT (if I understand it correctly) and when you save a prediction to the precise slot, it will save it for all the predictions for any mob. Same for model. So I couldn't use the lock slots to solve this in this case.

You can have memorized slots match nbt - available in settings.

I am going to close this as the functionality is expected as I explained and the minor change to insert into specific empty slots in some cases would likely not help many times because the stack would end up stacked with something else anyway.