Lets take a different approach to this problem. An aerospace fighter bay is something that is going to allow the fighter to fly off at various points that the dropship is on the move. A fighter is an object that takes up space as well. A fighter that is not going to be used until the dropship has landed does not need to go into the ASF bay since it is not going to try and defend, so think of it being moved in a strictly cargo hauling dropship moving cargo from world to world and unloading the fighter.
Think of what kind of set up that ASF bay is going to require to launch the fighter while the dropship is on the move. Probably something in some way akin to what you might see in starwars star destroyer, or that of battlestar galactica.
Depending upon the vtol and how it operates it might very well be possible to use it within an ASF bay while in atmosphere. Something that is similar to the karnov, a vtol with wings that uses rotar fans instead of a traditional helicopter style craft would probably work as it would be essentially fired out of the dropship and it's wings would allow it the lift needed to give the fans enough time to kick in, assuming the atmosphere at the point of the launch is heavy enough, I would assume. I would suggest that you probably could use the ASF bay as such.
When it comes to simply storing a vtol in a dropship, I would believe that it would easily fit into a vehicle's slot without a problem. This is likely true for standard vtols such as the warrior, pinto, and so on that are helicopter designs where their rotor blades can be strapped down. The karnov on the other hand could pose a problem depending upon the wings length, even if they can be folded upwards.
I would assume that the vehicle bays are semi modular so that they can accomodate vehicles of different sizes, but even if not I cannot imagine that most vtol's would be dramatically taller then a 100 ton tank.
As for simply stuffing a vtol into the cargo hold of a dropship, that has to be a given since there are likely bigger objects that need to be moved. Dropships are massive, they clearly dwarf mechs, so why shouldn't something the size of a vtol not be able to be loaded?
The question you need to ask is what kind of a priority the vtols will be once your ship has hit the ground. You answered that by saying you want them up and running for recon. If that is the case just how fast do you want them scouting things out? If you want them out there immediately then you would want them in an area where you know that vehicles are being prepped for deployment once the ship has landed, not where the big and bulky cargo is going to be. How you would transport the vtols may even differ. You might want to find a cargo container for the vtol since you don't want it to try and stress it when moving it along, which probably involves the use of a crane and other heavy machinery. Also, how much of a problem would it be to sort through it and other cargo, get it fueled and possibly armed and in a position where the crew is able to hurry the heck up and get out there.
I would say that if you want to use them when you land, you need them in a vehicle bay so that all preparations can be done before hitting the planet and so that the crew can easily get to it. Now if you are transporting vtols from planet to planet just as cargo to be handed off to someone else to use, then crate that sucker up and stuff it in the cargohold.
