Ahhhhh I know what it is, how could I be so dumb. I should have known as soon as you said bottom layer, and when I saw your silkscreen.
Ok, so you really should build all of your footprints on the top layer, regardless of whether they will be on the bottom of the board. Here is why, when you build a footprint on the top layers you are consistent across all of your libraries, and pretty much any library you will find. This is important because when you place a component whether you built it on the bottom or top, it will be placed on the top of the board. This means that the component body clearance is on the top of the board. This is why you are getting a collision error. Altium thinks that component is on the top of the board, when in reality you want it on the bottom. The solution is to draw your footprint on the top layers and then place and lower it to the bottom of the board pressing the L key while dragging it. Note the difference between the custom pad I made and then lowered.