yeah you are right
some partitions are broken probably from TWRP because a lot of users faced issues similar with yours
someone posted a solution few days ago how to boot a rom from sdcard
he had also broken partitions in internal memory caused from TWRP and he managed to boot a rom from sdcard
he created two partitions
one to be recognized as /data and one to be recognized as /system and mounted them successfully(if i remember well)
but i can't find that post
if i find it i will come with edit
Here is the link to the thread:http://forum.xda-developers.com/htc-...ssues-t2859588
Posted in Q&A as I didn't had privileges.
PS: I have to add some e2fsck commands as well as after some time the log starts showing warnings on mounts in the log but phone working ok.