Yes there is a difference. M2.3 is usually linked to the CPU so you will take away 4 lanes from there.
The first two are usually connected to the chip set and do not affect your PCIe lanes.
Mainstream Intel CPUs only have a pathetic 16 lanes. Use 4 of those for an M.2 drive and there goes any hope of running your graphics at x16
Additionally each M.2 connector on many motherboards are shared with your SATA ports, reducing the number of SATA drives you can connect.
Gigabyte have never been about transparency (They don't provide motherboard block diagrams), so it's sometime hard to tell, but as a general rule of thumb M2_3 will come from the CPU