It’s possible that when you defined the preset, you didn’t check the boxes ‘include font’ and ‘include font size’. If you didn’t, then applying the preset will have the effect you found. You just need to highlight text in the correct format and Format > Formatting > Redefine Preset from selection and make sure those settings are checked.
Do you mean Inline Footnotes / Annotations, or the ones in the Inspector? I’m not sure you can hide the text of either, but you can change the background colour to be less intrusive.