If your tranny and oil pans stick out into the air stream, sacrifice the extra bit of airflow, and clearance your undertray for them...
If you later decide you'd like to chance it awhile, you can always make some nice scoopy kinda things that cover them up, just make them removable until you're sure they won't have any effect.
IF either has vanes on it, it's designed to help cool, end of story. That doesn't mean its' actually necessary, but that's the intention. With Honda cars, it's pretty common that they have more cooling capacity than necessary, especially if you're only using it as a DD and not really working it out.
BTW, temp gauges are cheap... and trans temp gauges arent that expensive either... might be a good investment if you're worried about your trans.
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