While I get that its appropriately sci-fi to have a transporter room, and mechanically something is needed to make docking easier for large ships, I feel there is an existing mechanic begging to be expanded in to this role; cargo shuttles. Outside of the happy occurrence of a partial station production chain
within one system, cargo shuttles get very little use, and this is a hugely thematic use for them; kind of like the truck which turn up with its own forklift tucked up the back. I understand that lag concerns will be involved in anything of this sort, but those could be minimized by having only a token cargo shuttle transfer the goods, and the mechanic balanced by 'Transport' software maximum range as it is currently (perhaps its a 'Logistics Software & Tech Package' rather than de-atomiser software) so that the players are limited in range by their systems upgrade and in speed of transaction by the max velocity of their cargo shuttles.