Regarding stored parasite craft damage control: Would it be possible to have the mothership divide its damage control rating by the number of parasite craft needing repair, thereby limiting the possibility of exploiting large DC ratings in motherships?
Regarding underway replenishment systems: I would propose that there's a 1 hullsize component called an Underway Receiving Station that can receive the efforts of 1 of the Cargo Shuttles, Refueling Systems and Ordnance Transfer Systems each, but the component is entirely passive; it cannot transfer out on its own. On the other hand it has no upper limit of its own; it's entirely dependent on the providing component(s) of the donating ship(s). This works well with Transfer Hub equipped stations by design. Every Cargo Shuttle, Refueling System or Ordnance Transfer System component can give 1 more 'dock' in their specific transfer form, limited to their own rating.
Ships would with this proposal need at least 1 Underway Receiving Station for craft to craft transfers and it would be part of any new design that is created, same with the bridge component. Ships without this component need to either enter a hangar, which allows them to draw from their berth as if they had a single Underway Receiving Station, or enter orbit of a planet with an appropriate ground side supply structure for the same, or land on said planet, again for the same benefit.
And yes, this means that a ship that has lost its supplies, fuel and its Underway Receiving Station, if they had any, would need to be tugged back to a station or planet for repairs. This does not seem like a flaw.