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I don't play Grey Knights, but the answer to your question depends on the codex. I think in most cases it would cost the same amount of points, but taking them separately takes up more slots. Sisters of Battle can only take rhinos/Immolators as dedicated transports, for example. No option for taking the vehicle empty. Orks, on the other hand, can use trukks and battle wagons as dedicated transports, but can also take empty trukks as Fast Attack choices and battle wagons are Heavy Support options when taken alone. When a vehicle is taken as a dedicated transport, it counts the same as the unit it was purchased with. If you buy a Rhino as a DT for Troops, the Rhino counts as a Troop unit once the unit disembarks. Really useful in a CAD where Troops have ObSec.
I'm not certain of this, and don't have access to my rulebook for a few more hours, but I'm pretty sure you can take a vehicle as a dedicated transport and deploy it separately from the unit it came with, but no other units may start the game deployed within that vehicle. Only the unit that it was purchased with has the option of deploying inside the vehicle. Again, that could be wrong, you can look it up in the rulebook in the section for transports.
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