Encoded -superior glyphs for .sups feature

I know it is not recommended to put encoded glyphs in OpenType features. Reportedly it changes the original text string and causes issues with changing fonts. However I could not reproduce this problem. Can anyone help me determine in which applications or environments do these problems occur?
I am trying to establish if it’s possible to use the encoded -superior figures instead of unencoded .sups figures for the superscript feature. I noticed Glyphs will automatically use -superior glyphs if .sups are not available.

It’s a principle of OpenType to separate characters from glyphs, and the font will not touch the character stream. However, there are some exceptions that allow “change of semantic value”, and sups is one of them.

Thanks for the answer and the source link. Would the same be true for modifier letters? For example, putting amod (uni1D43) in the sups feature instead of a.sups? Glyphs does not put them in even as fallback.

No, it would not.