I don't think we can ever answer the former (my best guess is that there is something in the background of the stadium that works well with his deceptive pitching motion; there was an analysis long ago of why San Jose Municipal Stadium has a much higher strikeout rate and Giants hitters (including Bowker), noted that there were mountains in the background in CF that hid the ball in some visual haze plus also the sun would set in CF in the second half of the season and the hitter would be looking into the sun, so there was no hitter's eye, making it harder for the hitters to see the ball) but let's take a look at his monthly stats and see what's there.
Sometimes a chart tells a thousand words. As one can see in his OPS, it just get steadily worse and worse, until he's pretty bad in Sept/Oct. And his ERA mirrors that mostly, though as one can see, his OPS almost linearly gets worse, but there is a big jump in ERA once he gets to July, and the bigger jump in Sept/Oct. His BABIP mostly mirrors that, as well as his K/BB (or SO/W in the chart), except for his odd improvement in peripherals in August, but still worsening ERA and OPS. So it appears to be fatigue.
The thing is, I'm not sure what else he can do to combat that. It helps now that he's in a temperate ballpark, so we'll see if he can avoid the second half decline at home this season. He is known as an innings eater, that is a big reason we signed him, but it might behoove the Giants not to ride him too hard, if the relievers are well rested and needing work.
The Reds appear to have kept an eye on him, his pitch count was actually lower by 1.6 pitches in H2 vs. H1. He also pitched about a third of an inning less, probably as the result of giving up so many more hits and XBH's. Still, his PQS fell from 3.91 to 3.31 and Game Score fell from 62 to 56, from H1 to H2. He's giving up much more homers, though, only up slightly, and it was still very good, from 5.5% to 5.8%.