Why aren't chapters being added to my m2ts using tsmuxer?
M2TS as a format / container is not able to store chapter information itself. On Blu-Ray disks, the chapter data is stored in the playlist files. Therefore you won't see chapters when you just load an M2TS file in a player.
I am actually a total newbie to this, so I have no clue whether tsMuxeR creates appropriate playlist files when producing the ISO file. If so, you should see the chapters when you load the playlist file into the player, not the M2TS file.