Every time I run Kdenlive, I have to reload my custom layout. I've already set it to the top of the list, but that does nothing.

Is there a way to make it open my custom layout automatically when I start the program? This is annoying.

I assume you work with 20.08.xx. Give your custom layout a name (view -> save layout). Then goto view -> manage layouts and move your layout to the top. Now you should see your layout name top right and it should load as you start Kdenlive.