Hi @avalaughlin25,
As Jarmo pointed out, you can edit the platform presets file directly from its location on disk. Alternatively, you can make edits to your saved platform preset definitions by holding down the shift key before clicking on the preset icon > Customize Menu..., which will reveal the preset code section in the menu editor for you to make changes. Ordinarily that's not something we suggest, but in some cases it's useful which is why we have that method available.

However, I'm sorry to say that the customizations you wish to make are intentionally scrubbed during the application of a platform preset. Most axis settings, including reference lines, are usually context specific, and so in our research developing platform presets, it was determined that in most cases it would be problematic for us to retain them.
That said, we're considered some configurability about the scope of what a preset it able to set in a platform. If this functionality is something that would be helpful to you, adding it to our JMP Wish List can get it on our radar for future development!
@jules