I personally don’t think there is one silly question. Sometimes there are bad answers. I am not the smartest guy in every manner, sometimes I have to be corrected in opinions or or just how things work if I don’t understand them correctly…
Regarding the MIDI outputs, especially USB ones: Some USB MIDI devices have feedback control (i.e. corresponding lighting LEDs assigned to a switch like an AKAI APC) or they can process data that is sent to them. Imagine a USB MIDI device that needs to be connected to an USB host but has for example a CV Out port that is manipulated from within the host.
Unfortunately some of these devices use what is called system exclusive messages (messages for this specific device). You need extra functions for them that are not so well documented to work properly. There are some topics here regarding this (corresponding LEDs to a footswitch controller, to name it).
Other USB MIDI devices already use OSC messages that are easier to read out and are well documented. But these need a driver as well to lit up the corresponding LED to a switch.
I am not a programmer myself but I can read code. If you have a specific device you want full control (as it is within MacOSX or Windows) even a driver for the Mod linux system has to be written. In this case it is good for a programmer if she/he has access to that device.
The hardware MIDI input and output might be just for convenience, but I as a keyboard player use it everyday. I can play @x42’s setBfree and other synths within the Mod Duo from my masterkeyboard and my other rack synths (Access Virus A, Kurzweil PC2R, Emu Vintage Keys, Roland XV-5080). I have an expression pedal hooked up on my Nord Electro and I control the wah frequency with it. Here is the corresponding pedalboard.
If someone else might talk about the status of USB MIDI controllers I want to know more about it, too.
Feel free to ask in detail or more specific what the matter is…
Have a nice day and God bless, Marius