Another method to get it working, reported by Mash, is to delete the Config folder from My Documents\My Games\XCOM2\XComGame\Config

I can't seem to get the new overwatch/pod trigger feature to work, and I don't know what to do

You will need to edit XComGotchaAgain.ini, usually located in C:\Program Files (x86)\Steam\steamapps\workshop\content\268500\866874504\Config, like described in: http://psteamcommunity.yuanyoumao.com/workshop/filedetails/discussion/866874504/135512931363650067/

To enable the Overwatch and Pod triggers, you will need to set the following three variables to true: bUseCustomPathIndicatorSystem, bShowOverwatchTriggers and bShowActivationTriggers. I recommend also setting bShowVIPSpottedByEnemyIndicators to false when you do this, since they are not needed if you're using the activation trigger.

Be aware, that there are still some issues with the custom path-indicator system I created, specifically tiles are being reported as being on fire for a few turns after the fire died out, so there will be false fire-indicators if you enable this!

All of those are set to what you said, but it's still not showing in the game for me, for some reason

I can only propose you try the steps from the original + first post

Okay, this is weird, it works then it doesn't, then it does... I'm confused

I have a bug with LW2(v1.2) after update from GA v1.21(in this version I didn't have this bug) to the latest version.
If I open soldier's abilities screen from the armory(Armory-View soldiers-[soldier]-Abilities), then loads a vanilla abilities screen(2-way perk tree) instead of LW2(3-way perk tree). If I open abilities screen after mission(by clicking level up button), then loads normal LW2 abilities screen(3-way).
I tried to launch game only with LW2 and GA, it's not helped. I tried to delete the Config folder from Documents\My Games\XCOM2\XComGame\Config, it's not helped. I tried to begin new company, but it's not helped too. When I disable GA, the bug is missing.
It's a bug or I do something wrong?
Screenshot: http://imgur.com/a/AX7vh
UPD:
I found other bug(with PCS)
Screenshots with GA: http://imgur.com/a/Hpd1b PCS description is unavailable and available less PCS
Screenshots without GA: http://imgur.com/a/HiK4m PCS description is normal and available more PCS
I tried to change localisation, but it's not helped. Before the update, this bug did not exist too.

@Ilyuha2000 I am working on a update containing quite a few fixes as well as some new features, and one of the fixes is for this strange bug in interacting with LW2 that only happens for some people...

New version uploaded that fixes the bug described by Ilyuha2000

delete the Config folder from My Documents\My Games\XCOM2\XComGame\Config
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
That fixed completely non working mod state for me, i had absolutely no flanking indicators before this, thanks!

As of Aug 1st this mod stopped working as intented. None of the indicators except for Regular Shootable Indicator works. I've tried unsubbing & resubbing the mod. It did not work. I've also tried deleting XCOM2\XComGame\Config files twice now. The mod works for the Gatecrasher mission, then ceases to work again past that mission.