Anyone know of any risks to our tandem if we lay it flat in the back of our pickup?

None other than damage from sliding around. You'll want to pad under it and tie it in place securely. Another option is to fasten a QR carrier (Yakima Blockhead or similar) to a 2X4 that's wedged or secured in the truck bed.

We've carried our tandem horizontal in the back of our car for years.

FWIW if you're trying to avoid the roof rack, I have put mine on my hitch rack on my truck and it did just fine. I can see the rear wheel sticking out a few inches, the front wheel I tied sideways. A tandem is around about eight feet long before you take off or turn the wheels, minus a foot if you take off or turn the front wheel, minus another foot if you take off the back wheel. A full size truck is about 6.5 feet wide, a light truck about 6.

Some minor wear and tear wherever it touches the pickup bed is all. I carry my single bike in the van that way. Put the derailleur side up.

Why not get a bracket to attach the fork to the front of the pickup and stand it upright. There are many such devices available. Why let it roll around in the back of a pickup, that is just asking for damage.

Attach a rope to the tandem and your bumper. That way if/when it bounces out you can drag it like Chevy Chase

Thanks for tips. Sounds like I can cover the back with a Tonneau cover and avoid getting a topper.

There are front fork racks for pickups, we used to have one.

If it is a prized possession then obviously a little padding under the bike would be nice. Also, pedals aren't meant to take much side load abuse, so resting your tandem on them and bouncing down the road would not be a good thing for the pedal bearings. Resting on the pedals also creates a stress point on the end of your crank arms which are built more for rotational loads and not hammer hits from the side.

When we travel in our motorhome, we slide our Calfee into the bays underneath. I do remove the non-drive pedals, and captain's seatpost w/stoker bars, and obviously remove the front wheel too. Plus I place some deep foam under the rear triangle & crank arm and a protective cover over the front bars/shifters. Front wheel goes into a wheel bag. This process takes me less than 10 minutes to store or remove and setup. FWIW, I do the same with our singles.

We have always preferred to travel with bikes inside our vehicles rather than exterior racks.

We have fork mount rack in back of truck. I leave tailgate down and put front wheel in back seat. If we are pulling our camper, I put tailgate up. The rear wheel will rest on top of tailgate.

^^^ sure, but if he wants a Tonneau cover it's a mute point

Tie downs will hold it in place,
Cheap tiedowns? Old innertubes!!!