I think the downside of seatpost/stem is that it's more easy to check. Good point about RF, didn't consider that. I still think it's within the realms of possibility though?
Maybe they don't need to be hidden that well. If one or slip past then you can track those to the warehouse and send a few people to jail.
After that people can add fake trackers (maybe an antenna lead under the seat). Now the thieves have extra uncertainty, raising the cost to steal. And working trackers will be mixed in with the fake ones, making each bike a gamble.
This strategy works well in biology. Have one brightly coloured poisonous frog and then there are three or four mimics who are not poisonous (poison requires lots of resources!). Sure, some frogs still get eaten, but the mere threat of poison reduces the risk.
Maybe built into/epoxied to the inside-facing-side of crankset arms? Such that it looks like an expensive power meter crank. Definitely within the realm of possibility and I have heard that people have successfully done it as a DIY approach.
After that people can add fake trackers (maybe an antenna lead under the seat). Now the thieves have extra uncertainty, raising the cost to steal. And working trackers will be mixed in with the fake ones, making each bike a gamble.