The only built-in font with any glyphs from
Latin Extended Additional is Kobo Nickel, it is not very complete, but it displays the glyphs it has. I have a few sideloaded fonts that have some of those glyphs and they display okay too.
If the font has the glyphs then I think they'll be displayed, it shouldn't matter whether the font is built-in, sideloaded to the device, or embedded in an epub.
Edit: Attached are screenshots from my Glo (fw 3.16.0) displaying an epub table of unicode characters U+1E00 - U+1EFF. On the left is the built-in Kobo Nickel font, and on the right a sideloaded TeX Gyre Bonum font: