For example Westbrook is the most severe groundballer in MLB, and the last 3 years he has pitched 210+ innings each year, and given up just 19, 19, and 15 HR each year, respectively. I don't credit him twice, I just see a guy who limits flyballs and thus limits homers. In this case HR/9 and GB% work together and paint a clear picture.
In short, I almost never want a flyballer - his HR/9 will be high and this will bloat his ERA. If his HR/9 is NOT high, he has been either lucky or he pitchers at a big park like Petco. In that case, like I said earlier, I can give him a pass.
As I said in the initial post, it's nigh-on impossible, with a decent sample size, for a flyballer and a groundballer to have both the same K/BB and HR/9. In order to limit his homers, the flyballer must be putting far fewer balls in play. So, if the two have the same HR/9, the flyballer being better is a more likely explanation, along with park factor, as you rightly indentified (but then, if the flyballer is playing in the same park as last year, that shouldn't matter).
For what you say about flyballers and ERA, substitute 'groundballer' and WHIP. My point is that a) there is enough of a track record there that HR/9 gives us a perfectly good account of his ability to limit homers without needing GB/FB and b) even with that, he gives up so many balls in play that he still isn't that good a pitcher. His career WHIP is 1.39, and he's put up a sub-4 ERA over a full season only once. And that's in a pitcher's park.
These stats are virtually identical (slightly inferior) to Brett Myers' career numbers, and Myers is a flyball pitcher in a very small park.