Intonation without context
Remember that the intonation with most instruments in the orchestra doesn’t work like a piano where you simply hit a key and the resulting pitch is perfectly in tune. Rather there is with all notes a variability in how high or low the resulting pitch is. Musicians always orientate themselves at the musicians around them to fit into their sound and intonate properly with them. For an orchestrator that means that the trickier it is for a musician to find one’s pitch in a sound, the more problematic the intonation becomes. It is much easier for musicians to intonate with consonant intervals around them (e.g. two trumpets sitting next to each other playing a third apart is way easier for them than intonating a minor second apart). Of course it is not possible to look out for everybody when orchestrating music with complex harmonic structures but it really helps a lot to keep an eye out for such things and make life easier for your musicians by giving them rather consonant intervals between neighbouring players. This technique also works in massively dissonant sound structures. As long as you give musicians who are sitting close to each other (e.g. trumpet section) an easily understandable sound they can still create a nice dissonance with another section etc. The strategy should be to avoid (which is not always possible) musicians needing to find their place in a sound without any understandable reference for them to hang on to.