Do non-fluff painted models bother you?

[Mr Mystery]

Again that's breaking WYSIWYG, while sensible proxying (all Lascannons are Missile Launchers etc) isn't.

All about consistency.

[Deadlift]

Don't care how you paint your Plastic Crack, some originality and creativity is cool. But I do insist on WYSIWYG, only to save confusion.
Any colour is better than grey plastic.

[Wildeybeast]

Seconded. That's why everything I play with is basecoated.

[Xaric]

Hulk smash

[onlyonepinman]

And this is where it could be a problem as already mentioned.
Not too different from: "..and this Flamer is a plasma gun, but this one isnt. The melta over there is actually a missile launcher and the one next to it has Plasma instead of a Bolter.
It can get really confusing to keep track in a game where certain players can't even remember which psyker had which powers or even the current turn number.

Does WYSIWYG extend to colour schemes? Sensible proxying aside, if remembering that the CSMs on the table are green Khorne CSMs and not Nurgle CSMs is a struggle for someone, perhaps a game as complex as 40k isn't for them.

[Kirsten]

paint them however you want to. they are your models, you dropped the cash for them, paint them however you like. Khorne troops typically wear red, but not exclusively, it isn't like Khorne wrote a list of murder laws or anything.

[Psychosplodge]

I bring you these fifte.. ****** *smash*, ....ten, ten murder laws...

[Kirsten]

silly Splodgey, there must only be eight murder laws...

[Psychosplodge]

oops yeah forgot about that

[Charon]

Does WYSIWYG extend to colour schemes? Sensible proxying aside, if remembering that the CSMs on the table are green Khorne CSMs and not Nurgle CSMs is a struggle for someone, perhaps a game as complex as 40k isn't for them.

No, it does not but it CAN lead to confusion.
So this green marines are actually khorne marines, while these green marines are indeed nurgle marines, the pink and purple over there are nurgle too, the green ones over there are unmarked and these greens are Tzeentch.

WYSIWYG is also not a big problem if it is just "all special weapons are plasma guns". Simple and easy to remember. Just mixing them up can lead to confusion.
So if I would go for "the opposite" color scheme, I would make sure that it is easy to spot what the unit actually is. There is a reason why people tend to place "placeholder minis" next to their 5 identical Rhinos to keep track which units sit in which vehicle.
A little bit of clarity does both sides a favor.