All settings can be changed in-game via Mod Config Menu: Screenshot.
This requires the Mod Config Menu mod to be installed, which can be found on the workshop here. If Mod Config Menu is not installed the settings can be changed from XComGotchaAgainDefaultSettings.ini, located in "C:\Program Files (x86)\Steam\steamapps\workshop\content\268500\866874504\Config" by default, where you can change the following:

bShowSquadsightHackingIndicator: Enable/disable showing the hacking-indicator for units that are hackable or damagable with Haywire Protocol, Combat Protocol or Full Override because of another units vision.

bShowFriendlyLOSIndicators: Enable/disable the LOS indicators towards friendly units.

bShowVIPSpottedByEnemyIndicators: Enable/disable the indicators for controlled VIPs when they will be spotted by an enemy unit. This is not really necessary if using the the pod activation indicators.

bShowLoneWolfIndicator: Enable/disable the Lone Wolf indicator (has no effect without Long War 2).

sIconPack: Set this to the name of the iconpack to use. Currently the following are available, see the Workshop screenshots to see what they look like: lewe1, lewe2, lewe3, lewe4, lewe5, vhs0, vhs1 and vhs2.
I recommend using either vhs2 which is used by the mod as default and fallback, or lewe5 that has icons looking a lot like the vanilla ones.

bShowTowerHackingArrows: Enable/disable the hacking indicators for ADVENT towers.

bHideTowerArrowsAfterHacking: When set to true, the ADVENT tower indicators will be removed completely after a tower has been hacked, thus preventing any tower from being hacked. If set to false, the icon will change to indicate that hacking is not possible at all.

bShowRemoteDoorHackingIndicators: Enable/disable showing the doorhacking indicators when remote hacking is possible.

bShowLOSIndicatorsForGrappleDestinations: Enable/disable showing the LOS indicators when selecting a destination for the grapple ability.

bDisableHideObjectiveArrowsWhenUsingGrapple: Enable/disable hiding of objective arrows when selecting a grapple destination.

bDisableDimHostileUnitFlagsWhenUsingGrapple: Enable/disable dimming of hostile unit flags when selecting a grapple destination.

bUseCustomPathIndicatorSystem: Enable/disable the custom path-indicator system that is required to show indicators for overwatch and pod activation triggering.

bShowOverwatchTriggers: Enable/disable the indicators for triggering overwatches.

bShowOverwatchTriggerForSuppression: Enable/disable showing the overwatch trigger when running a suppression.

bShowActivationTriggers: Enable/disable the indicators for triggering pod activations.

bShowNoiseIndicators: Enable/disable the indicators for breaking windows and kicking in doors while not concealed.

bShowSmokeIndicator: Enable/disable the indicator for when the destination tile contains smoke.

bShowPsiBombIndicator: Enable/disable the indicator for when the destination tile is within the AOE of an active PsiBomb.