If I understand correctly, your FixLine handles ligatures and glyph substitutions? Is that the the part of the RTL mode in TextMesh Pro didn’t work properly?
In regards to your initial question, starting with Unity 2018.1, TMP will be provided via the new Unity Package Manager. This new version will include source code which will enable you to make the modifications you need.
Note this new version of TextMesh Pro uses a new set of GUIDs and FileIDs and as such will require projects to be convert with included Project Files GUID Remapping tool. See this thread for more details.
FYI: The new Text System (a.k.a. integrated version of TMP will include full support for OpenType Font Features which is essential for most non Latin based languages.