Welcome to the forum, Bethel.
Do you have a link to the product you're planning to use?
I've set a few u-channels in the curb when the tile is set. I siliconed the channel directly to the waterproofing layer, then to the tile on both sides.
If this is your plan, you should verify that the glass doesn't extend past the channel, as it does with some manufacturers for different reasons.
Also make sure that the channel is free of burrs and sharp edges that might puncture the waterproofing.
It's never a good idea to drill into a horizontal surface in a shower, so good on you for planning ahead.