On my 3x9 setup I tend to not like using the big and small cogs regardless of what chain ring I am using. I'm not a strong enough rider to spin out on 50-12 combo, even if it's a descent, I'd just as soon coast down it, and there aren't enough big/long hills around here for me to go to 30/28...actually not quite true with the latter as once in a while I take a gravel track that has a crazy 15-20% short ascent. But as a rule or habit I like to stay in the middle of the cassette.

Cross chaining is fine for brief periods as others have commented. I wouldn't over think it too much.