The xx in MGNR3xx/A is a regional designation. If you search for MGNR3D/A, you will mainly find hits in Germany, so the "D" probably stands for this region. If you search for MGNR3SM/A, you will find hits in Switzerland.
The German grey import currently costs 797.-, the domestic version 700.-.
The device itself will probably be the same. The warranty is also the same, Apple doesn't make any difference in which country you bought the device. But maybe there are differences in the accessories? The power cable will be the same, as the Mac Mini has a two-pin small appliance socket (IEC C7). So all that's left is the enclosed paper documents, which might be different.
So it doesn't matter, take the cheaper one.