Whirly:
Putting the controls on the desk was my way of avoiding any doubt when hiring from a couple of places where I wasn't so well known. (Can't be accused of "letting your mates have a go" if the controls are on the desk.)
Where I fly now and am well trusted this is less of an issue and they do sometimes go under the seat.
Totally agree that whoever flies it next should always check they have been put back in OK: I always make a point to tell the next pilot or the operator that I've had the duals out.
Also take the point that the fewer pointy bits under your bum the better - but if you have to take the wheels with you where else to put 'em ?