RoyBell wrote:
It may not be as cheap of an option, but I would opt for building a "roof rack" and getting some rooftop bike racks that let you leave the front wheel on.
You can use some 2x4s and conduit and attatch the racks to the makeshift roof rack. Fasten/strap it to the floor and you should be golden.
The potential problem with this, as the OP can attest to, is that you don't want to mount expensive bikes to roofs where they can be seen and a potential theft target. Now, if you're saying build a makeshift roof style rack that goes inside the trailer, completely different story. I've actually done that and used a PVC "2x4" fencing post with Yakima mounts on it. And that includes using a thru-axle adapter.
I've got a high end Yeti full-suspension MTB, 4" fatbike, hardtail and road bike and looking to buy a dedicated downhill MTB as well (can someone say Angel Fire!!!), none of those bikes are cheap and I'd hate to get them stolen. So finding ways to mount them inside is paramount and it also keeps road grime off them as well. Surprising how easy it is to get direct mounts to something like the PVC board as when the board is wide enough, it is not going anywhere. Take some foam and place between the rear frames of the bikes in case there is any "walking". I've done this in the bed of my truck that had a canopy on it. Same could be done inside a TH although I'd probably take motorcycle straps and secure the "lot" to avoid the trailer bouncing.
I did notice that this thread is a number of months older, someone may find useful info out of it.