It's in the Materials section of given effect, blendop= defines how the alpha channel (transparency) on tga file is proceeded and rendered
here's an example from vehiclefireeffect.ini effect in EE3:
[VehicleSmokeMaterial]
EffectShaderName=effectLightLevel.fx
DepthBufferCheck=TRUE
DepthBufferWrite=FALSE
IgnoreRenderOrder=FALSE
AlphaTestEnabled=FALSE
LightEnabled=FALSE
UseLightLevel=TRUE
SpecularEnabled=FALSE
EmissiveEnabled=FALSE
AmbientColor=1.000000,1.000000,1.000000,1.000000
DiffuseColor=1.000000,1.000000,1.000000,1.000000
ZBufferOffset=0.000000
PriorityLevel=3
BlendOp=BLEND_SRC_ALPHA <-here
NumTextureStages=1
TextureStage[01].TextureName=EE3_MB_L_smoke.tga
TextureStage[01].MipMap=FALSE
TextureStage[01].FilterEnabled=TRUE
TextureStage[01].StageColorOp=TEXTURE_MODULATE_DIFFUSE
TextureStage[01].StageAlphaOp=TEXTURE_MODULATE_DIFFUSE
[VehicleFireMaterial]
EffectShaderName=twColor1.fx
DepthBufferCheck=TRUE
DepthBufferWrite=FALSE
IgnoreRenderOrder=FALSE
AlphaTestEnabled=FALSE
LightEnabled=FALSE
UseLightLevel=FALSE
SpecularEnabled=FALSE
EmissiveEnabled=FALSE
AmbientColor=1.000000,1.000000,1.000000,1.000000
DiffuseColor=1.000000,1.000000,1.000000,1.000000
ZBufferOffset=0.000000
BlendOp=BLEND_INV_SRC_ALPHA_ADD_SRC <-here
NumTextureStages=1
TextureStage[01].TextureName=EE3_Expl3_Ani9.tga
TextureStage[01].MipMap=FALSE
TextureStage[01].FilterEnabled=TRUE
TextureStage[01].StageColorOp=TEXTURE_MODULATE_DIFFUSE
TextureStage[01].StageAlphaOp=TEXTURE_MODULATE_DIFFUSE
note not all effects have the materials defined in them