The Trekker 52 contacts the lids. There is enough flex in the OEM pannier box/lid that you can still wiggle it past. I didn't like it so I just dropped the cash on the much better constructed 33L Trekker side cases which makes getting stuff in/out much easier, and all keyed alike.
I just picked up a 52L Givi trekker topcase with OEM panniers, I used spacers and still cannot get the topcase high enough to clear the box, very frustrating. I'm hoping Tusk will someday make racks for their tusk panniers that pop off.
The Givi Trekker 33 and 46 liter cases are the same dimension in length and height. The 46 liter is three inches wider or thicker. I'm using a 46 liter as a trunk and really like it as a trunk. However, I don't have Yamaha side cases so I can't answer your question on clearance. Below is a link to an extra 46 liter case I'm selling, in the "for sale" section which has some pictures.