The TOC issue is a known bug in mobile ADE: it always uses the default font to display the TOC. I don't think there is any work around, although it just occurred to me that there is a very small chance that redefining the default font (serif) in the CSS might work:
font-family: "MSYaHei", serif, sans-serif;
The simplest fix for this can only be done by the vendor: replace the very limited Adobe font with a better font (e.g. better unicode coverage) as the default. I am surprised that Infibeam isn't already doing this on the Pi, but perhaps Netronix is providing their firmware support. It is my understanding that Adobe is OK with the device vendors doing this, but most don't bother to do so.
The choti matra bug can probably only be fixed by Adobe. It is caused by the choti matra coming after the letter it applies to in the text stream, but before it on the screen. So this isn't fixable with a font change.