I use clear and green bottles with my homebrews as usually one of three tester bottles. It's easier to see if there's some sort of bad stuff going on in the bottle.
That being said, it's not a bad rule to avoid clear and green bottles. Green bottles for a saison can add an interesting funk and in a good way! I made a saison about 2 years ago and my tester bottles had a certain funk over the brown bottles (that comparison got me fairly lit up) and I decided if I make another saison, I'd use as many green bottles as I had on hand.
Right, though when you use clear or green glass bottles for homebrewing I take it your brew is probably not seeing much sunlight?
Clear bottles for use as testers seems legit, for the reasons you mention.