It is a known limitation in VeSys Classic, one that does not exist in 2.0 . With Classic the inline is treated as a single object, with an attribute for the MALE/FEMALE name.
VeSys was intended to function in the way you described. The reason for this was that some of the users required the same Connector ID on either side of an inline, to support this VeSys allows you type in the Connector ID in one field and its applied to both connectors. This is quite a quick and easy way to do this and it would be interesting to see how you place and apply the same Connector ID's in VeSys 2.0
Looking at your drawing it appears that you have an inline between 2 connectors which are in the same harness and from your comments you don't want both sets of wires to be joined in an inline? If you could explain what you are trying to show then there is likely a workaround for this limitation.