Would you upload the sketch (the .fzz file) please? Upload is 7th icon from the left on the reply menu. At a quick look at the svg, it likely isn’t formatted correctly for a custom svg (although I’m not the expert on that either). Hopefully @opera_night who is much better at these will comment. This is usually tricky and hard to get right, although @opera_night has a number of posts on how to do it in the forum. The holes need to be dragged on to pcb layer from the pcb View section of core parts (the right hand window in Fritzing) or specified in the copper1/copper0 layers of a part. You likely want the first option here. I don’t think you can make them as part of the cutout custom svg (but I could be wrong). The keep-out is automatically generated from the parts, it isn’t a specifiable layer. There are tricks you can do with substituting mask layers from different gerbers to make odd mask requirements work, which involve generating a mask that does what you want (usually by removing something from the sketch) then coping the gerber it creates in to the real sketch’s mask gerber file.
Peter