Yes, it does make a difference (disconnecting them, that is), but we should start a new thread if we want to argue about that.
Electrically, using the SMA integrated disconnect is no different than using any other combiner designed for grounded systems. (It really should be called the SMA Integrated Disconnect and Combiner, but I guess that's too long for everyday.)
The inverter actually only has one input.
I believe that how the inverter detects ground faults is not relevant. AFAIK SMA doesn't make single phase inverters with multiple MPPT inputs (unlike, say, Power One), so all strings are ultimately combined whether it is transformerless or conventional. All GFDI action (at least with Sunny Boys) happens inside the inverter, after strings are combined, regardless of the type of inverter. You can combine the strings remotely or close to the inverter, and combine + and - at the same place or separately, with both types of inverters, according to your pleasure.
What needs to be said is that, even if you run all your DC + and - conductors to the inverter, you cannot use only the regular SMA integrated disconnect to combine your strings for a transformerless inverter. The reason has nothing to do with ground fault detection, rather it is that the SMA integrated disconnect lacks overcurrent protection on both sides of the circuit as required for ungrounded systems, and this is a code violation. You need to use something like the combiner that SMA offers precisely for such a purpose, which has fuseholders for both negative and positive conductors. I believe this is merely a matter of meeting code and making the system relatively safe in case of faults. That is, I believe that if you did use the regular SMA integrated disconnect on their transformerless inverter, the GFDI would still function properly, since that all actually happens in the inverter, not the disconnect, for both types of inverters.
If I were installing a system with an SMA transformerless inverter, I could, if I wanted, use a regular fused combiner at the array, one designed for a grounded system, but only combine the DC - conductors there, and pass the multiple DC + conductors through the combiner down to the SMA disconnect. It might even make economic sense to do that.