font silent substitution

Symbol font substitution has been a thing since the beginning and the days of PageMaker. Whenever a font did not have that specific glyph in its own set (most fonts back in the day didn't), Symbol stepped in. This included standard things like the © and ™.

So what you are seeing is normal behavior. Fonts eventually started to include these glyphs and, in the case of Pagemaker, you had an option to use one or the other.

InDesign, similarly, does this automatically, and of course newer fonts have them, so the symbol substitution doesn't happen. You will also notice there are no styles to the Symbol font... e.g. there is no Bold version.

To be clear, this is separate from the Missing Glyph Protection in Preferences > Advanced Type, which is meant to substitute another font (usually InDesign's default, say Myriad) if the typeface you were using was missing a multi-part glyph like particular accented character.

Missing glyphs are shown as pink boxes. Your greater-than-or-equal-to character isn't missing, it's in the STIX font. Why InDesign changed the font during PDF export is beyond me.