Just a few questions to help figure out what is going on here.
I was originally thinking you were baking in Blender, but it seems you are baking in Substance (hence the screenshots)? If you are using Blender, which engine are you using and if it’s Cycles, are you using a cage? Just want to make sure. 😉
While I haven’t personally tried baking in Substance for some time now, my initial thought would be that the bevel is not translating completely in Substance, and why you are not seeing the bevel with the modifier. If this is the case you may consider applying your modifiers, saving a copy of the blend as a “baking version”, and undo the apply to return your model to normal after.
On another note, I do know that some 3rd party 3D software package will translate the sharp marks. I cannot remember if Substance is one of them, but that could be something to keep in mind and used in place of the extra seams.
Those are just my initial thoughts and questions, and surely someone more aware of these issues can confirm or correct where needed. Best of luck!
