Don't forget that the Imperium runs on hypocrisy. Large percentages of the Adeptus Mechanicus is breaking their own rules, including working with abominable intelligences. In fact, what they are dealing with in their main factory world in Mars is a supposedly secret abominable intelligence. And it is, in fact, a shard of an alien god that turned other races into synthetic robots. Banned in public, the center of their cult in reality, even if many probably don't understand what in the world they are doing.

So yes, anything that is supposed policy in the Imperium is supposed to be taken with buckets of salt.