But the thing I worry about, having never been there, is that I might get some good recommendations for out-of-the-way spots where there would be few if any other tourists, and take the time to go find them, only to be denied entry because I’m a foreigner.
I also remain convinced most of the anti-foreigner tourism sentiment is anti-Chinese tourism sentiment. For westerners who can behave, it's still a great place to visit. (Though skipping Kyoto wouldn't be a bad idea.)
Yep, that's the part I hate, too. The locals put up completely understandable roadblocks to preserve their own culture, but those roadblocks end up making the whole situation hostile and unpleasant for anyone who is not known to the locals.
Since you've never been, let me just say this: most tourists are utterly clueless, so just not being clueless goes far. Blend in, imitate the locals' behaviors, try to speak the language, eat what you're given, etc., and you'll be fine. For now, at least, relatively few places ban foreigners outright.
Clothing and makeup is a better giveaway than facial features or skin tone, but even that is becoming harder with K-pop creating a pan-Asian style to aspire to.
Demanding the locals to accommodate your lazyness is basically shouting "I'm entitled".
You can still blend in far more than most tourists do by a) watching the people around you, and b) being a little bit self-conscious.
It's absolutely astounding how much tourists stand out in Japan (or Paris, or London, or New York...), and it's mostly about their behavior and clothing. Ten minutes of internet research and a little bit of introspection would go a long way to solving both problems.