It was due to x3 editor saving the pbd file with .txt extension. I corrected it and now model loads, allowed docking of m6+, allowed docking of a TS (superfreighter) with it, accepted a khaak fighter into its internal bay.
An additional superfreighter and an additional m6 were not able to dock though.
I sent one of the TS away, and an argon truelight seeker was able to dock in addition to already docked advanced heavy osprey.
So far seems to work quite fine.
Thanks to everyone who helped. im detailing the process i have gone through here for anyone who may need this in future :
- Opened x3 editor, with x3 AP profile.
- I chose Open from VFS, and found TShips.pck under types folder, and opened it.
- Scrolled down to Split Elephant and selected it
- In its Model tab, in front of Ship Scene, i saw that "ships\Cadius\Split\TL_Elephant_scene" was listed.
- I went to 'open from vfs', went down to 'objects\Cadius\Split' and opened 'TL_Elephant_scene'
- It asked me to open this with '3d Viewer', instead i went to "All" tab, and chose 'text viewer' instead, and opened with it.
- Noticed two blocks of lines with word 'dock' in it :
P 17; B ships\props\tstp_extdock_dummy; N ships\props\tstp_extdock_dummy; // idx 17
{ 0x2002; -61071; 5142; -157437; 0.000000; 0.000000; 0.000000; 0.000000; -1; 1; } // 0
P 18; B ships\props\tstp_extdock_dummy; N ships\props\tstp_extdock_dummy; // idx 18
{ 0x2002; 61071; 5142; -157437; 0.000000; 0.000000; 0.000000; 0.000000; -1; 1; } // 0
- I found the scene file for Yaki Ryu with the SAME procedure, and opened its scene file
- Opened this file with the same method 'text viewer'
- Observed two blocks of lines for docking :
P 24; B ships\props\extern_TS_dock; N Bships\props\extern_TS_dock; b // idx 24
{ 0x2002; -20901; -93875; -297586; 0.000000; 0.000000; 0.000000; 0.000000; -1; 1; } // 0
P 25; B ships\props\extern_TS_dock; N Bships\props\extern_TS_dock; b // idx 25
{ 0x2002; 20930; -93875; -297586; 0.000000; 0.000000; 0.000000; 0.000000; -1; 1; } // 0
- I took the parts after the first ';' for first lines from each block from Elephant scene file like this :
B ships\props\tstp_extdock_dummy; N ships\props\tstp_extdock_dummy; // idx 17
B ships\props\tstp_extdock_dummy; N ships\props\tstp_extdock_dummy; // idx 18
- And then replaced these into the same places (after first

in the Ryu scene file so it became like this :
P 24; B ships\props\tstp_extdock_dummy; N ships\props\tstp_extdock_dummy; // idx 17
{ 0x2002; -20901; -93875; -297586; 0.000000; 0.000000; 0.000000; 0.000000; -1; 1; } // 0
P 25; B ships\props\tstp_extdock_dummy; N ships\props\tstp_extdock_dummy; // idx 18
{ 0x2002; 20930; -93875; -297586; 0.000000; 0.000000; 0.000000; 0.000000; -1; 1; } // 0
- I didnt change anything else.
- Then, for ryu scene file, i went to save as from menu, then chose 'switch to system dialog' and then saved it under Top X3 directory under 'objects\ships\yaki' with a different name 'yaki_TL_scene_m6docking.pbd'
- Whatever you do the x3editor saves the file with .txt extension added. you have to go there manually from windows and correct the filename to yaki_TL_scene_m6docking.pbd from yaki_TL_scene_m6docking.pbd.txt
- after that i went to the yaki ryu entry in TShips.pck i opened before, to model section, and changed the value for Ship Scene from 'ships\Yaki\Yaki_TL_scene' to 'ships\Yaki\Yaki_TL_scene_m6docking'
- I directly clicked save, and saved the TShips.pck directly as it was, (via vfs), and overwrote what was in there
- I launched the game, reloaded an earlier save, bought a Ryu from yaki shipyard, and i was able to dock my m6s.
...........
hopefully this will help someone in future.