I think order manipulation is very effective against warp.

I can say that you can repair and fortify border between materium and immaterium.

With order knowledge psykers can develop own power and not transform into warp portal.

Order is rational indeterminacy inducement.

If some warp entity want take your soul they can't just invade your mind and steal you from material plane. They must invent material mechanism that can steal souls with some request accomplished.(cursed artefacts that want you agree with user policy of certain entity's)

You can't just lose control with order power because order is polar antagonist of warp that not work as solid construction or even liquid system , warp is clouded sky of colored emoji fields with own IQ, and I'd that sentient field want to interact with you it need agree with your user policy.

But not forget most ancient law of nature , law of power. If your order is simple or weak powered you must prepare to shit breach on your side.

Necrons know about warp nature ( they killed old ones that was masters of psionics in cosmic scale) and they know how to affect to laws of material world to strengthen order of reality and not allow warp even make appearance near their technology.

They want to kill you but they can't . Emperor of mankind is do the same thing he take power from them and sit in material universe near psi augmentation Instrument. If they want come and take revenge they not leave in healthy condition .

One vs one imperor can win because he have power equal to one of them at least for sure.

All worship of humanity goes strait to emperor and support him as warp god but there many underwater stones.

But considering would the user be a huge target in the Warp's watchlist

Not bigger then other big warp entity's.+ Order manipulation allow you become less bright in warp. You can look like just materium psykers (little lamp) or become almost undetectable because your order power not allow chaotic nature do without causes and any detection must be detailed and precise.

Nice but how about primordial order though how would that be