If you play with coins, these cannot be visually identified as anything. There are no irritating clashes of one thing representing another thing, because everything is nothing.
If you play with grey plastic, the only visual identification is by race/model range. A grey marine is a generic marine, a grey ork is a generic ork. You only get clashes with visual identification if you use an ork as an eldar or similar.
Both of the above examples have no in-game visual identity. They have no fluff in their looks. The marine has no chapter, the ork no klan. The exception is if the grey model is covered in chapter/klan-specific iconography. That counts as a pseudo-paintjob in terms of identification.
Once the model gets paint, it assumes a visual identity in the game. You can easily ignore this identity, just like you can easily play with coins or unpainted models. But since most people start playing because they are attracted to the visual identity of models, it creates annoyance in many people when the paint suggests one identity and the rules suggest another. This annoyance can be mitigated with explanatory fluff and theme, and worsened by appearances of a WAAC attitude.