[Jellby]

The proper way to deal with ligatures is not using them in your text, but rely on the rendering software to pick them when available. In other words, don't write anything special for "Th", "ffl" or "st", just write the usual individual letters. If you use a font that has ligatures for these combinations but the reader is not displaying them, complain to those responsible of the rendering software, the book itself is right.

By the way, note that in your sample, calibre is not using the same font (that's why some of the glyphs are not available), look at the W shape. As for splitting some ligatures, I think there is some checkbox to disable this.