Selecting the same uboat type and date allows SH3Cmdr to copy in the uboat and date based files relevant to the mission (for example, if you select VIIC/41 the correct model will be loaded, which wouldn't be the case had you just selected the boat type in SH3). Selecting Flotilla doesn't do much, just ensures the right water textures are loaded (even though IIRC Flotilla isn't an option in SH3 single missions, if you intend running a Med based mission you could select the appropriate Flotilla in SH3Cmdr to ensure the correct water textures are loaded).
SH3Cmdr really is aimed more at the campaign player, though.
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