In the VBAM/Starmada book: The Stars Divided: Terran Civil War, ships carried internally by a tender took a Capacity of their Hull size + 50% of their Hull size. It is a minor point, that needs to be settled by an arbitrary decision, whether this should have an additional cost in Space Units of 50% or 25%.
In the Starmada Compedium, there was a rule for towing vessels that should work just as well for composite vessels made of multiple Hulls. Multiply the Engine Value of each module by the Hull Size of that module, add the results for all modules with Engines, and divide by the sum of the Hull Sizes of all modules (including those without engines). This would give you the Engine Value for the Composite. Alternatively, you could consider the modules as components contained in a Hull whose size is large enough to contain them, sum the Space Unit cost for the Engines in all modules, and divide this (rounding down) by the Space Unit cost for a Engine for the containing Hull. This would also give a useful Engine Value for the composite.
In any case, Hold Capacity on a Tender should affect only the Space Unit cost. The Combat Rating of the contents should have no effect on the Combat Rating of the Tender (which, if it is unarmed, might well be zero).