The system is solid, but it does need to be done correctly. If you are DIYing it I recommend going to sal diblasi on YouTube and looking it up there. He has a wealth of information on all things tile related. More on reddit.com

Did you measure to see that the difference in what you planned for height was 1/4” or are you basing that on the notch size difference solely? I would definitely check to be sure before I started trying to fix the issue. If it is 1/4”, I would put down 1/4” cement board. 1/4” plywood is likely to delaminate. I used it once at the direction of my boss (before I knew any better) laid ditra down, came back the next day to find literal hills in it. Had to tear up the ditra and the 1/4” plywood and redo. Keep in mind however that since cement board on a floor must be bedded in mortar, you’re going to end up with more than 1/4”. Personally I would try to make this work rather than risk the 1/4” ply. Or rip up the pan and put down a new one. They aren’t cheap for sure but choose your battle I guess. More on reddit.com

If you bring it to level with self leveling, use a primer before you use mortar to install the shower pan or you will have bond issues. The pan itself has the proper slope once level. With the curb, you can cut it down or leave it depending on look. It is easier to level with a stiff mortar. I fill the underside 2/3 up so it holds the curb in place. The corner kits to seal the curb should be done last to avoid moving it by accident. Just remember to put a gentle slope into the shower to avoid water running out of the shower under the door.

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You want waterproofing in this area, not just water resistance, and definitely not something organic that will rot. Once you lay down mortar and tile, you can drive a forklift over the schluter trays. More on reddit.com