Now I can confirm what I wrote last time. The "CE Vanilla Player Ship Loadouts Addon" disables enemy AE content like ships and weapons. There is no chance for them to generate during run. I did about five runs (one to second sector and one to fourth) and nothing generated. Then I disabled this addon and after that I got for example auto ship with mind control.
There's my mod order once again:
10 Better Planets and Backgrounds 1.3.1
11 Better Asteroids
20 Extra Names Mod 1.1
40 CE Resource Pack 1.246
41 FTL Captains Edition 1.248
42 CE BPaB Compatibility Patch 1.0
50 CE Additional Music Addon 1.248
60 EL Texture Pack 1.24
61 CE Endless Loot Addon for standard CE 1.247
70 CE Vanilla Player Ships Loadouts Addon 1.214b
80 Shiny! UI Overhaul 0.98 CE
81 Ain't Nobody Got Time For That Replacer
82 BetterShipColorNightmareEdition
83 Highres Shields 1.1
90 Random Flagship
And I found strange thing about this station:
http://zapodaj.net/5b9de928081f5.bmp.html
It surrenders just after starting battle. I met it 2 times to confirm that.